Antimicrobial peptides : methods and protocols

ME T H O D S IN MO L E C U L A R BI O L O G Y Series Editor John M. Walker School of Life Sciences University of Her...

Author: Andrea Giuliani | Andrea C. Rinaldi

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ME T H O D S

IN

MO L E C U L A R BI O L O G Y

Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK

For other titles published in this series, go to www.springer.com/series/7651

TM

Antimicrobial Peptides Methods and Protocols

Edited by

Andrea Giuliani Spider Biotech, Colleretto, Giacosa, Italy

Andrea C. Rinaldi University of Cagliari, Monserrato, Italy

Editors Andrea Giuliani Spider Biotech S.r.l. Via Ribes, 5 10010 Colleretto Giacosa TO Bioindustrypark del Canavese Italy [email protected]

Andrea C. Rinaldi Università di Cagliari Dipto. di Scienze e Tecnologie Biomediche 09042 Monserrato Cittadella Universitaria Italy [email protected]

ISSN 1064-3745 e-ISSN 1940-6029 ISBN 978-1-60761-593-4 e-ISBN 978-1-60761-594-1 DOI 10.1007/978-1-60761-594-1 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2009943247 © Springer Science+Business Media, LLC 2010 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Humana Press, c/o Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. While the advice and information in this book are believed to be true and accurate at the date of going to press, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. Cover illustration: Inset image adapted from Figure 2 of Chapter 13. Background image adapted from Figure 3E of Chapter 15. Printed on acid-free paper Humana Press is part of Springer Science+Business Media (www.springer.com)

Dedicated to the memory of Silvano Fumero, poet and scientist. (Andrea Giuliani) On April 6, 2009, an earthquake devastated the town of L’Aquila, in Italy, taking the lives of more than 300 people and marking indelibly those who survived. This book is dedicated to the memory of the victims, and, as a warm wish, to all those, including some of the authors of the present volume, that will have to build their future from scratch. (Andrea C. Rinaldi)

Preface As our knowledge of the innate immune systems in multicellular organisms has grown steadily in the last two decades, so has our comprehension of the basic role played by gene-encoded, ribosomally synthesized antimicrobial peptides (AMPs) in this ancient line of defense against infections. Indeed, although the ability of many prokaryotes to produce and release peptidic or proteinaceous substances with antibacterial and antifungal activity has been known for quite a long time, the presence of AMPs in humans and animals (and later plants) has been recognized only more recently, in the 1980s, with the identification of cecropins in the pupae of Hyalophora cecropia moth, defensins in human neutrophils, and magainins in skin secretions of the frog Xenopus laevis (1–3); these findings, though, were grounded on previous work conducted in the 1960s and 1970s, for example, by Hussein Zeya and John Spitznagel. Since then, the quest for new AMPs has gifted us with many hundreds of biologically active peptides, extremely varied in sequence and structure, isolated from virtually every multicellular organism where they have been looked for (4). Visiting the several available web-based repositories dedicated to AMPs – such as AMSDb (http://www.bbcm.univ.trieste.it/∼tossi/pag1.htm), ANTIMIC (http://research.i2r.a-star.edu.sg/Templar/DB/ANTIMIC/), and APD2 (http://aps.unmc.edu/AP/main.php) – can help in getting a more precise idea of what “diversity” means in this case. By the end of the 1990s, AMPs research was already blooming. The first Gordon Research Conference on Antimicrobial Peptides was held in 1997 in Ventura, California, and these meetings have since been a privileged point of discussion and the cradle of many ideas around these intriguing molecules. The same year the GRC series on AMPs started, the first Methods in Molecular Biology volume dedicated to AMPs, edited by William Shafer, was published (5). From those early days, we have gone a long distance ahead, although the journey seems by no means to come to an end soon. Much has been learned about the mechanism of target selection and cell killing, always with the aim of transforming an evolutionary, successful, antimicrobial shield into the next century’s antibiotic drugs. Thanks to years of intense study in many public and private research institutions worldwide, many AMPs (in particular those of mammals) began to be recognized as endowed with more than simply direct antimicrobial properties, by acting at the interface between innate and adaptive immunity, for example, as immunomodulants, immunostimulants, and/or inducers of proinflammatory cytokines or chemokines, to the point that today many prefer to refer to these substances with the more general term of “host defense peptides.” Notwithstanding these major efforts, AMPs have not yet fulfilled their main promise, i.e., to be able to truly represent the next-generation antibiotics with new modes of actions. This is for a complex variety of causes that have collectively hampered clinical progress to date. Some of these are related with the peptidic nature of AMPs which translates, for instance, to poor bioavailability, poor proteolytic stability, and cost of goods issues, or with their mechanism of action, which might bear some potential for unwanted toxicity. A helping hand, in this sense, would probably come in the near future by the development of synthetic

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analogues of AMPs, with improved characteristics (and lower cost) with respect to their natural counterparts (6). For one that approaches this research area from outside, the truly multidisciplinary scenario it offers might at first sight be surprising and even a bit confusing. Immunologists, infectivologists, dermatologists, microbiologists, cell biologists, molecular geneticists, biochemists, peptide chemists, biophysicists, and many others with different scientific backgrounds have entered the arena, each one approaching the challenges on the table from a distinct point of view, while elaborating at the same time original perspectives for the field’s development. The medical potential of which AMPs are inherently endowed with certainly lies at the core of this interest, but it does not explain everything. In our opinion, a good fraction of the AMPs’ ability in catalyzing such a diversified attention relies on their privileged position at the center of a perfect storm, where scientifically mature fields such as antibiotics and immunology research on one side and membrane/peptide biochemistry and biophysics on the other one positively clash. On this stage, each field is in search of a new object of study for unleashing the potential of perfectionated equipment and theories, a reachable goal with important practical consequences, and, ultimately, an occasion for rejuvenation. In the present volume of Methods in Molecular Biology, we have attempted to provide an updated overview of this burgeoning field, by offering snapshots of the many different approaches leading scientists in the field follow to crack AMPs’ most hidden attributes and properties, with the ultimate end of harnessing the potential these compounds do display for applicative purposes. As in the series’ style (and name), most of the contributing chapters deal with experimental protocols, presented “in readily reproducible, step-by-step fashion.” In addition, several review chapters discuss in a more classic manner selected issues pertaining to different aspects of AMPs, namely the forms of interaction of AMP’s with the lipopolysaccharide (LPS) component of Gram-negative bacteria (Chapter 10), the diverse dynamic transitions peptides (not only AMPs, but also, for example, fusogenic peptides) may undergo in membranes (Chapter 13), and the therapeutic potential of host defense peptides (Chapters 19 and 20). As a reading guide, chapters are organized around three main themes: the isolation, purification, and production in recombinant form of AMPs from natural sources and the design and synthesis of unnatural compounds; the methodologies – of either biophysical, biochemical, or computational nature – usually applied to define AMPs’ molecular features and to explore their mechanism(s) of action; the studies focused on the biological activities (antimicrobial, anti-inflammatory, immunomodulatory, and so on) of AMPs, and on their use as therapeutic agents. Contributions gathered in the first part will lead the reader through the discovery of novel AMPs from sources as different as frog skin secretions (Chapter 1) and human skin (Chapter 2), and of lantibiotics from Gram-positive bacteria (Chapter 3). The production of recombinant antimicrobial peptides in bacteria is one of the possible routes to achieve an in-depth structure–activity analysis of AMPs, through selective and systematic removal and/or substitution of given residue positions, and a suitable strategy for the development of a less expensive peptide-production platform. Chapters 4 and 5 will thus discuss the production of AMPs by recombinant approaches in Escherichia coli. Approaches for the rational design of AMPs and for the production of peptide variants by solid-phase synthesis will be described in Chapters 6 and 7, respectively. Finally, the SPOT synthesis technique – a powerful tool offering the opportunity of synthesizing and screening a large number of peptides arrayed on a planar cellulose support – comes under focus in two different contributions (Chapters 8 and 9). With membranes apparently being an obligate passage in the action of all AMPs – whether

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exerting their activity through destabilization of the membrane itself or directed toward an intracellular target – it is not surprising that all contributions of the second part of the volume deal, in a way or the other, with membrane interactions of peptides. These can be characterized by taking advantage of sophisticated membrane model systems or live cells, tryptophan and lipid fluorescence, and a few selected fluorescent dyes, a combination that permits to carefully measure several aspects of membrane-binding and membraneperturbing activities of selected AMPs and peptidomimetics, as described in Chapters 11 and 12. Structural studies of AMPs, either alone or when embedded in a membrane environment, are unquestionably of pivotal importance, and in this context solid-state NMR is gaining momentum as a very informative technique, as underlined in Chapter 14 (see also Chapter 13 for more details on NMR studies). Besides NMR, microscopic techniques can also offer important clues in order to disclose more on AMPs function and cell specificity, providing a “whole-cell” perspective. Chapter 15 depicts how atomic force microscopy can be used to dissect the behavior of some AMPs (in this specific case, the so-called Sushi peptides from horseshoe crab), whereas Chapter 16 describes the use of a mix of fluorescence/electron microscopy techniques to get insight into the damage caused by AMPs on the morphology and membrane structure of intact bacterial cells. This section terminates with the important contributions coming from computational resources, in the form of molecular dynamics simulations (Chapter 17) and quantitative structure–activity relationships (QSAR) analysis of antimicrobial peptides (Chapter 18 for this approach see also Chapter 6). The third and last section of the book sketches just a few, although very significant, approaches put in force so far to disclose the medical and therapeutic potential of AMPs as anti-infective and immunomodulant agents. Single contributions deal with infection models and activity assay systems (Chapters 21, 22, 23, and 24), and with the characterization of the antimicrobial activity of peptides against the protozoan pathogen Leishmania (Chapter 25). Within the limitations inherent to the selection process of topics to be included in the present volume, which necessarily left over many important issues that would have deserved the same covering, we hope that the readers – either expert of the field or newcomers – will find in these pages both an authoritative guide for their own lab work on AMPs or related substances and a good load of thought stimuli to inspire their scientific endeavors.

References 1. Steiner, H., Hultmark, D., Engstrom, A., Bennich, H., and Boman, H. G. (1981) Sequence and specificity of two antibacterial proteins involved in insect immunity. Nature 292, 246–268. 2. Ganz, T., Selsted, M. E., Szklarek, D., Harwig, S. S. L., Daher, K., Bainton, D. F., and Lehrer, R. I. (1985) Defensins. Natural peptide antibiotics of human neutrophils. J. Clin. Invest. 76, 1427–1435. 3. Zasloff, M. (1987) Magainins, a class of antimicrobial peptides from Xenopus skin: isolation, characterization of two active forms, and partial cDNA sequence of a precursor. Proc. Natl. Acad. Sci. USA 84, 5449–5453. 4. Zasloff, M. (2002) Antimicrobial peptides of multicellular organisms. Nature 415, 389–395. 5. Shafer, W. M., ed. (1997) Antibacterial Peptide Protocols. Methods in Molecular Biology, vol. 78. Humana Press, Totowa, NJ, USA. 6. Giuliani, A., Pirri, G., Bozzi, A., Di Giulio, A., Aschi, M., and Rinaldi, A. C. (2008) Antimicrobial peptides: natural templates for synthetic membrane-active compounds. Cell. Mol. Life Sci. 65, 2450–2460.

Andrea Giuliani Andrea C. Rinaldi

Contents Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiii SECTION I:

ISOLATION, PURIFICATION, DESIGN, AND SYNTHESIS OF A NTIMICROBIAL P EPTIDES

1.

Antimicrobial Peptides in Frog Skin Secretions . . . . . . . . . . . . . . . . . . J. Michael Conlon and Agnes Sonnevend

3

2.

Purification of Antimicrobial Peptides from Human Skin . . . . . . . . . . . . . Jens-M. Schröder

15

3.

Strategies for the Isolation and Characterization of Antibacterial Lantibiotics . . . . . . . . . . . . . . . . . . . . . . . . . . . . Daniela Jabes and Stefano Donadio

31

Expression and Purification of Recombinant ␣-Defensins and ␣-Defensin Precursors in Escherichia coli . . . . . . . . . . . . . . . . . . . . . . . . . . . Sharel Figueredo, Jennifer R. Mastroianni, Kenneth P. Tai, and André J. Ouellette

47

Production of Recombinant Antimicrobial Peptides in Bacteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mateja Zorko and Roman Jerala

61

4.

5.

6.

7.

Methods for Building Quantitative Structure–Activity Relationship (QSAR) Descriptors and Predictive Models for Computer-Aided Design of Antimicrobial Peptides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Olivier Taboureau Synthesis and Thermodynamic Characterization of Small Cyclic Antimicrobial Arginine and Tryptophan-Rich Peptides with Selectivity for Gram-Negative Bacteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mojtaba Bagheri

77

87

8.

Synthesis of Antimicrobial Peptides Using the SPOT Technique . . . . . . . . . 111 Dirk F.H. Winkler and Kai Hilpert

9.

High-Throughput Screening for Antimicrobial Peptides Using the SPOT Technique . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125 Kai Hilpert

SECTION II: 10.

ANALYSIS, PROPERTIES, AND MECHANISMS OF A NTIMICROBIAL P EPTIDES

Antimicrobial Peptides: The LPS Connection . . . . . . . . . . . . . . . . . . . 137 Andrea Giuliani, Giovanna Pirri, and Andrea C. Rinaldi

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11.

Binding and Permeabilization of Model Membranes by Amphipathic Peptides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155 Paulo F. Almeida and Antje Pokorny

12.

Comparing Bacterial Membrane Interactions of Antimicrobial Peptides and Their Mimics . . . . . . . . . . . . . . . . . . . 171 Nathaniel P. Chongsiriwatana and Annelise E. Barron

13.

Dynamic Transitions of Membrane-Active Peptides . . . . . . . . . . . . . . . . 183 Stephan L. Grage, Sergii Afonin, and Anne S. Ulrich

14.

Solid-State NMR Investigations of Membrane-Associated Antimicrobial Peptides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209 Christopher Aisenbrey, Philippe Bertani, and Burkhard Bechinger

15.

Use of Atomic Force Microscopy as a Tool to Understand the Action of Antimicrobial Peptides on Bacteria . . . . . . . . . . . . . . . . . 235 Ang Li, Bow Ho, Jeak Ling Ding, and Chwee Teck Lim

16.

Fluorescence and Electron Microscopy Methods for Exploring Antimicrobial Peptides Mode(s) of Action . . . . . . . . . . . . . 249 Ludovica Marcellini, Maria Giammatteo, Pierpaolo Aimola, and Maria Luisa Mangoni

17.

Molecular Simulations of Antimicrobial Peptides . . . . . . . . . . . . . . . . . 267 Allison Langham and Yiannis N. Kaznessis

18.

Computer-Based Analysis, Visualization, and Interpretation of Antimicrobial Peptide Activities . . . . . . . . . . . . . . . . . . . . . . . . 287 Ralf Mikut

SECTION III:

ANTIMICROBIAL PEPTIDES AS THERAPEUTIC AGENTS

19.

Potential Therapeutic Application of Host Defense Peptides . . . . . . . . . . . 303 Lijuan Zhang and Timothy J. Falla

20.

Therapeutic Potential of HDPs as Immunomodulatory Agents . . . . . . . . . . 329 ˚ Havard Jenssen and Robert E.W. Hancock

21.

Assay Systems for Measurement of Anti-inflammatory Activity . . . . . . . . . . 349 Evelina Rubinchik and Christopher Pasetka

22.

Ex Vivo Skin Infection Model . . . . . . . . . . . . . . . . . . . . . . . . . . . 359 Evelina Rubinchik and Christopher Pasetka

23.

Measuring Antimicrobial Peptide Activity on Epithelial Surfaces in Cell Culture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 371 Gill Diamond, Sunghan Yim, Isaura Rigo, and Laura McMahon

24.

Antimicrobial and Antibiofilm Activity of Quorum Sensing Peptides and Peptide Analogues Against Oral Biofilm Bacteria . . . . . . . . . . . . . . . 383 Karen LoVetri and Srinivasa Madhyastha

25.

Characterization of the Leishmanicidal Activity of Antimicrobial Peptides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 393 ´ Luque-Ortega and Luis Rivas Juan Roman

Subject Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 421

Contributors SERGII AFONIN • Karlsruhe Institute of Technology, Institute for Biological Interfaces (IBG-2); Institute of Organic Chemistry, Karlsruhe, Germany PIERPAOLO AIMOLA • Dipartimento di Biologia di Base ed Applicata, Università di L’Aquila, L’Aquila, Italy CHRISTOPHER AISENBREY • Institut de Chimie, CNRS, Université de Strasbourg, Strasbourg, France PAULO F. ALMEIDA • Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC MOJTABA BAGHERI • Leibniz Institute of Molecular Pharmacology (FMP), Berlin, Germany ANNELISE E. BARRON • Department of Bioengineering, Stanford University, Stanford, CA BURKHARD BECHINGER • Institut de Chimie, CNRS, Université de Strasbourg, Strasbourg, France PHILIPPE BERTANI • Institut de Chimie, CNRS, Université de Strasbourg, Strasbourg, France NATHANIEL P. CHONGSIRIWATANA • Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL J. MICHAEL CONLON • Department of Biochemistry, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, UAE GILL DIAMOND • Department of Oral Biology, UMDNJ-New Jersey Dental School, Newark, NJ JEAK LING DING • Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore STEFANO DONADIO • NAICONS Scrl., Milano, Italy TIMOTHY J. FALLA • Helix Biomedix Inc., Bothell, WA SHAREL FIGUEREDO • Department of Pathology and Laboratory Medicine, School of Medicine, College of Health Sciences, University of California, Irvine, CA MARIA GIAMMATTEO • Centro di Microscopie, Università di L’Aquila, L’Aquila, Italy ANDREA GIULIANI • Research and Development Unit, SpiderBiotech S.r.l, Colleretto Giacosa, Italy STEPHAN L. GRAGE • Karlsruhe Institute of Technology, Institute for Biological Interfaces (IBG-2); Institute of Organic Chemistry, Karlsruhe, Germany ROBERT E.W. HANCOCK • Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada KAI HILPERT • Institute of Biological Interfaces – IBG 2, KIT (Karlsruhe Institute of Technology), Forschungszentrum Karlsruhe, Eggenstein-Leopoldshafen, Germany BOW HO • Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, Singapore DANIELA JABES • NAICONS Scrl., Milano, Italy

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˚ HAVARD JENSSEN • Department of Science, Systems, and Models, Roskilde University, Roskilde, Denmark ROMAN JERALA • Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia YIANNIS N. KAZNESSIS • Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN ALLISON LANGHAM • Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN ANG LI • Singapore-MIT Alliance (SMA), National University of Singapore, Kent Ridge, Singapore CHWEE TECK LIM • Division of Bioengineering and Department of Mechanical Engineering, National University of Singapore, Kent Ridge, Singapore KAREN LOVETRI • Kane Biotech Inc., Winnipeg, MB, Canada ´ LUQUE-ORTEGA • Centro de Investigaciones Biológicas (CSIC), Madrid, JUAN ROM AN Spain SRINIVASA MADHYASTHA • Kane Biotech Inc., Winnipeg, MB, Canada MARIA LUISA MANGONI • Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche, Azienda Ospedaliera S. Andrea, Università “La Sapienza”, Roma, Italy LUDOVICA MARCELLINI • Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche, Università “La Sapienza”, Roma, Italy JENNIFER R. MASTROIANNI • Department of Pathology and Laboratory Medicine, School of Medicine, College of Health Sciences, University of California, Irvine, CA LAURA MCMAHON • Department of Oral Biology, UMDNJ-New Jersey Dental School, Newark, NJ RALF MIKUT • Institute for Applied Computer Science (IAI), Forschungszentrum Karlsruhe GmbH, Karlsruhe, Germany ANDR E´ J. OULLETTE • Department of Pathology and Laboratory Medicine; Department of Microbiology and Molecular Genetics, School of Medicine, College of Health Sciences, University of California, Irvine, CA CHRISTOPHER PASETKA • MIGENIX Inc., Vancouver, BC, Canada GIOVANNA PIRRI • Research and Development Unit, SpiderBiotech S.r.l, Colleretto Giacosa, Italy ANTJE POKORNY • Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC ISAURA RIGO • Department of Oral Biology, UMDNJ-New Jersey Dental School, Newark, NJ ANDREA C. RINALDI • Department of Biomedical Sciences and Technologies, Cittadella Universitaria, University of Cagliari, Monserrato, CA, Italy LUIS RIVAS • Centro de Investigaciones Biológicas (CSIC), Madrid, Spain EVELINA RUBINCHIK • MIGENIX Inc., Vancouver, BC, Canada ¨ JENS-M. SCHR ODER • Clinical Research Unit “Cutaneous Inflammation”, Department of Dermatology, University Hospital Schleswig-Holstein, Kiel, Germany AGNES SONNEVEND • Department of Medical Microbiology, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, UAE OLIVIER TABOUREAU • Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark

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KENNETH P. TAI • Department of Pathology and Laboratory Medicine, School of Medicine, College of Health Sciences, University of California, Irvine, CA ANNE S. ULRICH • Karlsruhe Institute of Technology, Institute for Biological Interfaces (IBG-2); Institute of Organic Chemistry, Karlsruhe, Germany DIRK F.H. WINKLER • Brain Research Centre, University of British Columbia, Vancouver, BC, Canada V6T 2B5 SUNGHAN YIM • Department of Oral Biology, UMDNJ-New Jersey Dental School, Newark, NJ LIJUAN ZHANG • Helix Biomedix Inc., Bothell, WA MATEJA ZORKO • Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia

Section I Isolation, Purification, Design, and Synthesis of Antimicrobial Peptides

Chapter 1 Antimicrobial Peptides in Frog Skin Secretions J. Michael Conlon and Agnes Sonnevend Abstract Skin secretions from many species of anurans (frogs and toads) are a rich source of peptides with broadspectrum antimicrobial activities that may be developed into agents with therapeutic potential, particularly for topical applications. This chapter describes the use of norepinephrine (injection or immersion) to stimulate peptide release from granular glands in the skin in procedures that do not appear to cause distress to the animals. The peptide components in the secretions are separated using reversed-phase HPLC on octadecylsilyl-silica (C18 ) columns after partial purification on Sep-Pak C18 cartridges. Peptides with antimicrobial activity are then identified by demonstration of their abilities to inhibit growth of Gramnegative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria in liquid phase microtiter plate assays. Individual peptides with activity are purified to near homogeneity by further chromatography on butylsilyl-(C4 ) and diphenylmethylsilyl-silica columns and characterized structurally by automated Edman degradation and mass spectrometry. Key words: Frog skin secretions, antimicrobial peptide, reversed-phase HPLC, Escherichia coli, Staphylococcus aureus.

1. Introduction The emergence in all regions of the world of strains of pathogenic bacteria and fungi with resistance to commonly used antibiotics constitutes a potentially serious threat to public health and has necessitated a search for novel types of antimicrobial agent to which the microorganisms have not been exposed (1). Analysis of skin secretions from different species of Anura (frogs and toads) has led to the characterization of a wide range of peptides with biological activity that may have potential for drug development (2). Peptides with broad-spectrum antibacterial and antifungal activities and with the ability to lyse mammalian cells A. Giuliani, A.C. Rinaldi (eds.), Antimicrobial Peptides, Methods in Molecular Biology 618, DOI 10.1007/978-1-60761-594-1 1, © Springer Science+Business Media, LLC 2010

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Conlon and Sonnevend

are synthesized in the skins of species from certain, but by no means all, anuran families. These peptides represent a component of the system of innate immunity that defends the animal against invasion by pathogenic microorganisms (3) and have excited interest as candidates for development into therapeutically valuable anti-infective agents (4). Structural characterization of the frog peptides has shown that they comprise between 10 and 48 amino acid residues and a comparison of their amino acid sequences reveals the lack of any conserved domains that are associated with biological activity. However, the frog skin peptides, with few exceptions, are cationic because of the presence of several lysine residues and also contain a preponderance of hydrophobic amino acids particularly leucine and isoleucine. Circular dichroism and NMR studies have shown that they generally lack stable secondary structure in aqueous solutions but have the propensity to form an amphipathic ␣-helix in the environment of a phospholipid vesicle or in a membrane-mimetic solvent such as 50% trifluoroethanol–water (5). It is a common misconception that antimicrobial peptides are synthesized in the skins of all frog species. At this time, cationic ␣-helical antimicrobial peptides have been identified in the skins of frogs from species belonging to the Alytidae, Bombinatoridae, Hylidae, Hyperoliidae, Leiopelmatidae, Leptodactylidae, Myobatrachidae, Pipidae, and Ranidae families but several well-studied species from the Bufonidae, Ceratophryidae, Dicroglossidae, Microhylidae, Pelobatidae, Pyxicephalidae, Rhacophoridae, and Scaphiopodidae families do not appear to synthesize these peptides (reviewed in (6)). Skin secretions from South American and Australian frogs belonging to the family Hylidae (7) and North American and Eurasian frogs belonging to the family Ranidae (8) have proved to be particularly rich sources of antimicrobial peptides. The dermal peptides are stored in granular glands present in the skin and are released into skin secretions, often in very high concentrations, in a holocrine manner upon stress or injury as a result of contraction of myocytes surrounding the glands. In the laboratory or in the field, intradermal injection of norepinephrine (9) or immersion of the animal in a solution of norepinephrine (10) are effective methods for stimulating release of peptides into skin secretions that are well tolerated by animals and are the procedures that will be described in this chapter. Following initial fractionation by reversed-phase HPLC, peptides with antimicrobial activity are identified by measuring their abilities to inhibit the growth of reference strains of Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria in liquid phase in vitro assays. These peptides are purified to near homogeneity (>98% purity) by reversed-phase HPLC using columns containing a range of different packing materials. The primary

Frog Skin Antimicrobial Peptides

5

structures of the purified peptides are determined by automated Edman degradation and the proposed amino acid sequences confirmed by MALDI-TOF mass spectrometry. A general strategy for purification of peptides to near homogeneity by reversed-phase HPLC (11) and characterization of peptides isolated from frog skin by MALDI-TOF mass spectrometry (12) has been presented in recent articles. The major obstacles to the use of frog skin antimicrobial peptides as useful anti-infective drugs are their toxicities, particularly if they are to be administered systemically, and their short halflives in the circulation. However, peptides applied to infected skin or skin lesions in the form of sprays or ointments can penetrate into the stratum corneum to kill microorganisms so that future therapeutic applications are more likely to involve topical rather than systemic administration. Similarly, strategies have been developed for the design of analogs of naturally occurring peptides that show reduced cytolytic activity against mammalian cells while maintaining potency against microorganisms (13, 14).

2. Materials 2.1. Collection and Partial Purification of Skin Secretions

1. Norepinephrine bitartrate salt (Sigma-Aldrich, St Louis, MO, USA). 2. Distilled water. 3. Concentrated hydrochloric acid (36% w/v) (BDH, Poole, UK). This reagent is corrosive. 4. Sep-Pak C18 cartridges (Waters Associates, Milford, MA, USA). 5. Minipuls 3 peristaltic pump (Gilson, Middleton, WI, USA). 6. Speed-Vac concentrator with multi-tube rotor (Thermo Fisher Scientific, Waltham, MA, USA).

2.2. Reagents and Equipment for Preparative HPLC

1. Acetonitrile (HPLC Spectro grade, Thermo Fisher Scientific). This reagent is toxic. 2. Water (Milli-Q purified; 18.2 Mcm–1 ) or HPLC Spectro grade (Thermo Fisher Scientific). 3. Trifluoroacetic acid (99.8% purity; Sequenal grade, Thermo Fisher Scientific). This reagent is extremely corrosive and hand and eye protection should be worn. 4. An HPLC system capable of generating a binary gradient using pumps operating in the flow rate range 0.1–10 mL/min, a Rheodyne 7125 injection system equipped with a 2 mL loop, a detector capable of simultaneously monitoring at two wavelengths (typically 214 and 280 nm) (see Note 1).

6


5. HPLC columns: (a) (2.2 cm × 25 cm) Vydac 218TP1022 preparative C18 column (Grace, Deerfield, IL, USA), (b) (1.0 cm × 25 cm) Vydac 218TP510 semi-preparative C18 column, (c) (1.0 cm × 25 cm) Vydac 214TP510 semi-preparative (C4 ) column, (d) (1.0 cm × 25 cm) Vydac 219TP510 semi-preparative diphenylmethyl column. Preparative columns are used at a flow rate of 6 mL/min and semi-preparative columns at a flow rate of 2 mL/min (see Note 2). 6. Helium cylinder for degassing of solvents (see Note 3). 7. Gastight model 1002 2.5 mL injection syringe (Hamilton, Reno, NV, USA). 8. Polypropylene tubes 12 mm × 75 mm and 15 mm × 100 mm (Nunc brand by Thermo Fisher Scientific) (see Note 4). 9. 1.5 mL clear polypropylene Eppendorf tubes (e.g., Nunc). 10. Model 206 fraction collector (Gilson). 11. Freezone 4.5 lyophilizer (Labconco, Kansas City, MO, USA). 2.3. Reagents and Equipment for Antimicrobial Assays

1. Spectrophotometer able to measure at λ = 600 nm. 2. Microtiter plate reader able to measure at λ = 630 nm. 3. Incubator or 37◦ C constant temperature room for culturing microorganisms in air. 4. 15 mL sterile tubes with cap (Corning, MA, USA). 5. 96 well cell culture plates with lid (Nunclon Surface, Nunc). 6. Disposable semi-micro polystyrene cuvettes (1.5 mL) (BrandTech Scientific, Essex CT). 7. Mueller Hinton broth (Oxoid, Basingstoke, UK). 8. Tryptic Soy Agar solid media plates (Oxoid). 9. Bacterial strains: E. coli ATCC 25922 and S. aureus ATCC 25923 (American Type Culture Collection, Manassas, VA, USA).

3. Methods 3.1. Collection of Skin Secretions 3.1.1. Injection Procedure

1. Inject animals individually at two sites within the dorsal sac with a freshly prepared solution of norepinephrine in water (2 nmol/g body weight in a volume of 200 ␮L) (see Note 5). 2. Immediately after injection, place the animal for a period of 15 min in water contained in a covered glass beaker (typically 100 mL with a greater volume for particularly large specimens) (see Note 6).


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3. Immediately acidify the solution containing the secretions after collection with concentrated hydrochloric acid (final concentration 1% v/v) and store at –20◦ C until time of analysis (see Note 7). 3.1.2. Immersion Procedure

1. Immerse the animals for 15 min in a covered glass beaker to which has been added a sufficient volume of distilled water containing 200 ␮M norepinephrine to completely cover the frog. 2. Process the solution containing the secretions as in Section 3.1.1, Step 3.

3.2. Sample Preparation Using Sep-Pak Cartridges

1. Prepare HPLC solvent A by adding 1.2 mL trifluoroacetic acid to 1,000 mL water (see Note 8). 2. Prepare HPLC solvent B by adding 1.0 mL trifluoroacetic acid to 700 mL acetonitrile/300 mL water. 3. Activate Sep-Pak cartridges by pumping acetonitrile (2 mL per cartridge) at a flow rate of 2 mL/min using a peristaltic pump or manually using a 20 mL plastic syringe, followed by HPLC solvent A (2 mL/cartridge; see Section 3.2, Step 1). Up to 10 Sep-Pak cartridges may be connected in series depending on the volume and amount of peptide material in the extract to be processed. 4. Centrifuge the combined skin secretions and washings (5,000g for 30 min) (see Note 9). 5. Pump the supernatant through the Sep-Pak cartridges at a flow rate of 2 mL/min. If a peristaltic pump is not available, a polypropylene syringe (50 mL) can be used to apply the solution manually. 6. Pump HPLC solvent A (4 mL/cartridge) is pumped at a flow rate of 4 mL/min and discard the eluate. 7. Pump HPLC solvent B (2 mL/cartridge; see Section 3.2, Step 2) at a flow rate of 1 mL/min and collect the eluate into polypropylene tubes. 8. Reduce the volume of eluate to approximately 1.5 mL under reduced pressure in a Speed-Vac concentrator (see Note 10). With an efficient vacuum pump, this step can be accomplished in approximately 60 min at room temperature or in 30 min with external heating. Sample may be stored at 4◦ C overnight or frozen at –20◦ C for several days.

3.3. Peptide Separation by Reversed-Phase HPLC

1. Degass HPLC solvent A and solvent B (see Section 3.2, Steps 1 and 2) with helium for 1 min. This time should not be exceeded.

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2. Column preparation. Before injecting the sample, it is necessary to “condition” whatever column is to be used in order to improve resolution by following these steps: irrigate the column at an appropriate flow rate (see Section 2.2, Step 5) with HPLC solvent B for 20 min; decrease the concentration of solvent B to 0% over 10 min using a linear gradient; increase the concentration of solvent B to 100% over 10 min; decrease the concentration of solvent B to 0% over 10 min; equilibrate the column with HPLC solvent A for 20 min. 3. Centrifuge the sample for 5 min at 13,000g in a 1.5 mL polypropylene Eppendorf tube to ensure clarity of solution (see Note 11). 4. Program the HPLC system to perform chromatography under the following conditions using linear gradients for elution: (a) increase concentration of solvent B from 0 to 30% over 10 min; (b) increase concentration of solvent B from 30 to 90% over 60 min; (c) increase concentration of solvent B from 90 to 100% over 1 min and hold at 100% until UV-absorbance returns to baseline value (see Note 12). 5. Inject the sample onto the column. Up to 1.5 mL may be injected into a 2 mL loop. 6. Increase the concentration of solvent B according to the elution program listed in Section 3.3, Step 4. Collect fractions (1 min) into (15 mm × 100 mm) polypropylene tubes using a fraction collector (see Note 13). 7. Take aliquots (20–200 ␮L depending on the size of the UVabsorbing peak) of each fraction for determination of antimicrobial activity and dry under reduced pressure in 1.5 mL Eppendorf tubes using a Speed-Vac concentrator. 3.4. Purification of Antimicrobial Peptides to Near Homogeneity by Reversed-Phase HPLC

1. Replace the preparative C18 column used in Section 3.3 with a (1.0 cm × 25 cm) Vydac 214TP510 semi-preparative C4 column equilibrated with 30% HPLC solvent B (see Section 3.2, Step 2) at a flow rate of 2 mL/min. (see Note 14). 2. Reduce the volume of the fractions containing antimicrobial peptides (Section 3.3, Step 6) to approximately 1 mL in a Speed-Vac concentrator. Inject each sample onto the C4 column. 3. Raise the concentration of solvent B to 80% using a linear gradient (see Note 14). Collect major individual UVabsorbing peaks by hand into polypropylene tubes. 4. At this point, the peaks containing the peptide with antimicrobial activity are identified by the assay method described in Section 3.5 and purified further as described in the following steps.


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5. Replace the C4 column by a (1.0 cm × 25 cm) Vydac 219TP510 diphenylmethyl column equilibrated with 30% solvent B at a flow rate of 2 mL/min. 6. Reduce the volume of the fraction from Section 3.4, Step 3 to approximately 1.0 mL in a Speed-Vac concentrator. Inject the sample onto the column. Follow the same elution conditions as in Section 3.4, Step 3. 7. Collect the major UV-absorbing peak by hand into a polypropylene tube (see Note 15). 8. Freeze dry and weigh the purified peptide (see Note 16). 3.5. Detection of Peptides with Antimicrobial Activity

1. Inoculate reference bacterial strains (S. aureus ATCC25923 and E. coli ATCC25922) into Mueller Hinton broth (5.0 mL) in separate 15 mL sterile tubes and culture at 37◦ C for 4 h (logarithmic phase of growth). Sterile pipette tips must be used in all procedures. Determine the cell count (colony forming unit, CFU/mL) of the bacterial cultures by measurement of absorbance at 600 nm (see Note 17). 2. Dilute the cultures with Mueller Hinton broth to a 106 CFU/mL cell count. 3. Redissolve the Speed-Vac dried fractions from Section 3.3, Step 7 in 10 ␮L of 0.1% trifluoroacetic acid–water to which 100 ␮L of Mueller-Hinton broth is added. Distribute aliquots (50 ␮L) in duplicate into the wells of a 96 well microtiter plate (see Note 18). Fill at least four wells with Mueller-Hinton broth only (100 ␮L) for sterility control and fill at least another four wells with Mueller-Hinton broth only (50 ␮L) to serve as growth control. 4. Add the S. aureus ATCC 25923 suspension (50 ␮L 106 CFU/mL) to each individual well of one plate containing the reconstituted fractions and to the four wells containing 50 ␮L Mueller-Hinton broth only (growth control). 5. Add the E. coli ATCC 25922 suspension (50 ␮L; 106 CFU/mL) to each individual well of a second plate containing the reconstituted fractions and to the four wells containing 50 ␮L Mueller-Hinton broth only (growth control). 6. Incubate the microtiter plates at 37◦ C overnight (approximately 16 h) in a humidified atmosphere of air in an incubator or in a room at constant temperature (see Note 19). 7. Determine the bacterial growth by measuring absorbance at either 600 or 630 nm (depending on the filter installed) using a microtiter plate reader. The absorbance of the sterility control wells containing Mueller-Hinton broth only is taken as zero value. The absorbance of the growth control wells containing bacteria only is taken as the 100%

10


value. Peptides in chromatographic fractions that inhibit the growth of either bacterium by ≥50% are purified further, as described in Section 3.4 (see Note 20). In the example shown in Fig. 1.1, norepinephrine-stimulated skin secretions obtained from the Asian frog Hylarana picturata, after partial purification on Sep-Pak cartridges, were chromatographed on a (2.2 cm × 25 cm) Vydac 218TP510 preparative C18 column equilibrated with HPLC solvent A at a flow rate of 6 mL/min. The concentration of acetonitrile in the eluting solvent was increased as described in Section 3.3, Step 4. Aliquots (100 ␮L) of the major peaks in the chromatogram were subjected to antimicrobial analysis (Section 3.5) and the peaks designated 1–5 were shown to inhibit growth of both E. coli and S. aureus (15).

Fig. 1.1. Elution profile on a preparative Vydac C18 column of skin secretions from Hylarana picturata after partial purification on Sep-Pak cartridges. The peaks designated 1–5 were shown to contain peptides that inhibited the growth of both E. coli and S. aureus. The dashed line shows the concentration of acetonitrile in the eluting solvent. Subsequent structural analysis demonstrated that peak 1 contained brevinin-2PTa, peak 2: brevinin-2PTb; peak 3: brevinin-PTa and brevinin-2PTc; peak 4: brevinin-1PTb, brevinin-2PTd, and temporin-PTa, and peak 5: brevinin-2PTe. (Reproduced from (14) with permission from Elsevier Science).

4. Notes 1. A dual pen flatbed chart recorder (Kipp and Zonen, Delft, The Netherlands) to supplement any on-screen computer


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recording system is useful especially when there is a significant delay in the response of the absorbance detector and the appearance of the peak on the computer screen. 2. The decision whether to use a preparative or a semipreparative C18 column for initial fractionation depends upon the peptide content of the secretions. For samples containing > 10 mg peptide material, a (2.2 cm × 25 cm) preparative column should be used. The approximate amount of peptide material may be estimated using a BCA (bicinchoninic acid) protein assay reagent kit following the recommended procedure of the manufacturer (Thermo Fisher Scientific). 3. Degassing of solvents may be achieved although less efficiently by using an ultrasonic bath but degassing by reducing the pressure is not recommended as it may lead to relative loss of volatile components. 4. Polypropylene tubes should be used throughout, not glass or polystyrene, in order to minimize irreversible binding of peptides to the tubes. 5. The amount of norepinephrine injected is not critical but the agent is unstable in solution and so must be dissolved in water immediately before use. Animals that appear to be agitated or highly mobile can be partially anesthetized by immersion for 5 min in crushed ice. 6. Norepinephrine injection is generally well tolerated by the animals without signs of discomfort and fatalities are extremely rare. However, in the case of very small frogs, tadpoles, or protected or endangered species for which it may be impossible to obtain a permit to carry out an invasive procedure, the immersion procedure may be used. The agent is absorbed through the frog’s skin and stimulates peptide release, although with reduced effectiveness compared with injection. Alternative methods used to stimulate secretions include electrical stimulation (typically 10 V DC, pulse duration 3 ms) at multiple sites on the dorsal region (16) and confining the animal in a closed container containing ether (17) but these methods appear to cause distress to the frog. 7. If secretions are collected in the field, it may not be possible to freeze the sample immediately. In this case, secretions can be kept at 0◦ C in an ice bath for several hours until access to a freezer is obtained. 8. A slightly greater concentration of trifluoroacetic acid in HPLC solvent A than in solvent B produces a flat baseline under HPLC gradient elution conditions.

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9. Frog skin secretions contain lipid components but it is generally unnecessary to remove them by extraction with an organic solvent prior to partial purification on Sep-Pak cartridges. 10. The sample should not be dried completely except when this is unavoidable (e.g., for shipment to a different laboratory) as this can lead to formation of insoluble material and irreversible binding to plastic surfaces. 11. Filtering the sample is not recommended unless absolutely necessary as it can lead to appreciable loss of peptide by irreversible binding to the filter material. 12. At the end of the experiment, wash the column with acetonitrile (50 mL) and store in this solvent. 13. Fractions may be stored in stoppered tubes at –20◦ C for up to several months. However, peptides containing methionine and tryptophan residues may oxidize on prolonged storage, even at low temperature. 14. The majority of frog skin antimicrobial peptides are eluted from a Vydac C18 column in the concentration range of 55–85% HPLC solvent B. To purify the more hydrophobic peptides on a Vydac C4 column, raise the initial solvent concentration to 40% B and the final concentration to 90% B. 15. Peptide purity is assessed by a symmetrical peak shape measured at two wavelengths (214 and 280 nm) and by mass spectrometry. 16. It is necessary to use a freeze drier to obtain the purified peptide in a flocculent powder form that is suitable for weighing. This generally is not achieved when solutions are taken to dryness in a Speed-Vac concentrator. When amino acid sequence analysis is to be carried out in the chromatographer’s own laboratory or institute, it is preferable not to dry the fractions completely but reduce the volume to approximately 30 ␮L in order to minimize losses of peptide due to irreversible binding to the plastic tubes. When samples are to be analyzed by an external core facility, lyophilization to dryness cannot be avoided. 17. The first time a new bacterial strain is used, a standard curve of OD600 vs. CFU/mL is constructed using the following procedure: Prepare a series of eight double dilutions of a dense suspension (2.5 mL; OD600 > 1.5) of the bacterium in sterile 0.9% saline (1:2, 1:4, up to 1:256 dilution). Measure the absorbance at 600 nm of each dilution using disposable plastic cuvettes. Prepare a series of eight 10-fold dilutions of the same initial suspension (1:10, 1:102 up to


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1:108 dilution). Spread aliquots (200 ␮L) of the 105 , 106 , 107 , and 108 dilutions in duplicate onto Tryptic Soy Agar plates. Incubate the plates overnight at 37◦ C and count the numbers of colonies on each plate. Count only plates with >50 colonies. Calculate the cell count in the original bacterial suspension by multiplying the average number of colonies by the dilution factor. For example, if 78 and 86 colonies are counted on the plates prepared from the 106 dilution, the original cell count in the suspension is 82 × 5 × 106 = 4.1 × 108 CFU/mL (the factor 5 arises from the fact that only a 200 ␮L aliquot was used). Construct a standard curve where the logarithmic abscissa (X) represents the cell count (CFU/mL) and the linear ordinate (Y) represents the corresponding OD600 values. 18. It is better to use separate plates for different microorganism to avoid contamination. 19. The microtiter plates may be placed in a sterile polyethylene box with lid containing a paper towel moistened with water. 20. If required, the minimum inhibitory concentrations (MIC values) of the purified antimicrobial peptides can be determined by the microdilution method described in detail in (18). References 1. Norrby, S. R., Nord, C. E., and Finch, R. (2005) Lack of development of new antimicrobial drugs: a potential serious threat to public health. Lancet Infect. Dis. 5, 115–119. 2. Rinaldi, A. C. (2002) Antimicrobial peptides from amphibian skin: an expanding scenario. Curr. Opin. Chem. Biol. 6, 799–804. 3. Hancock, R. E. (2001) Cationic peptides: effectors in innate immunity and novel antimicrobials. Lancet Infect. Dis. 1, 156–164. 4. Conlon, J. M. (2004) The therapeutic potential of antimicrobial peptides from frog skin. Rev. Med. Microbiol. 15, 17–25. 5. Powers, J. P. and Hancock, R. E. (2003) The relationship between peptide structure and antibacterial activity. Peptides 24, 1681–1691. 6. Conlon, J. M., Demandt, A., Nielsen, P. F., Leprince, J., Vaudry, H., and Woodhams, D. C. (2009) The alyteserins: two families of antimicrobial peptides from the skin secretions of the midwife toad Alytes obstetricans (Alytidae). Peptides 30, 1069–1073.

7. Amiche, M., Ladram, A., and Nicolas, P. (2008) A consistent nomenclature of antimicrobial peptides isolated from frogs of the subfamily Phyllomedusinae. Peptides 29, 2074–2082. 8. Conlon, J. M., Kolodziejek, J., and Nowotny, N. (2009) Antimicrobial peptides from the skins of North American frogs. Biochim. Biophys. Acta 1788, 1556–1563. 9. Nutkins, J. C. and Williams, D. H. (1989) Identification of highly acidic peptides from processing of the skin prepropeptides of Xenopus laevis. Eur. J. Biochem. 181, 97–102. 10. Davidson, C., Benard, M. F., Shaffer, H. B., Parker, J. M., O‘Leary, C., Conlon, J. M., and Rollins-Smith, L. A. (2007) Effects of chytrid and carbaryl exposure on survival, growth and skin peptide defenses in foothill yellow-legged frogs. Environ. Sci. Technol. 41, 1771–1776. 11. Conlon, J. M. (2007) Purification of naturally occurring peptides by reversed-phase HPLC. Nat. Protoc. 2, 191–197. 12. Conlon, J. M. and Leprince, J. (2010) Identification and analysis of bioactive peptides

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in amphibian skin secretions. In Peptidomics Protocols and Methods Handbook. Soloviev, M. (Ed.), Totowa, NJ: Humana, in press. 13. Conlon, J. M., Al-Ghaferi, N., Abraham, B., and Leprince, J. (2007) Strategies for transformation of naturally-occurring amphibian antimicrobial peptides into therapeutically valuable anti-infective agents. Methods 42, 349–357. 14. Conlon, J. M., Galadari, S., Raza, H., and Condamine, E. (2008) Design of potent, non-toxic antimicrobial agents based upon the naturally occurring frog skin peptides, ascaphin-8 and peptide XT-7. Chem. Biol. Drug. Des. 72, 58–64. 15. Conlon, J. M., Kolodziejek, J., Nowotny, N., Leprince, J., Vaudry, H., Coquet, L., Jouenne, T., and King, J. D. (2008) Characterization of antimicrobial peptides

from the skin secretions of the Malaysian frogs, Odorrana hosii and Hylarana picturata (Anura:Ranidae). Toxicon 52, 465–473. 16. Tyler, M. J., Stone, D. J., and Bowie, J. H. (1992) A novel method for the release and collection of dermal, glandular secretions from the skin of frogs. J. Pharmacol. Toxicol. Methods 28, 199–200. 17. Lai, R., Zheng, Y. T., Shen, J. H., Liu, G. J., Liu, H., Lee, W. H., Tang, S. Z., and Zhang, Y. (2002) Antimicrobial peptides from skin secretions of Chinese red belly toad Bombina maxima. Peptides 23, 427–435. 18. Clinical and Laboratory Standards Institute (2006) Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria that Grow Aerobically (7th ed.). Wayne, PA: CLSI.

Chapter 2 Purification of Antimicrobial Peptides from Human Skin ¨ Jens-M. Schroder Abstract Human skin is a rich source of human antimicrobial peptides. Its cellular source is the keratinocyte, which terminally differentiates in the uppermost parts of the skin, eventually forming the stratum corneum, the horny layer. The easy availability of human stratum corneum makes it possible to identify and characterize human antimicrobial peptides with a biochemical approach. Moreover, the availability of lesional scales of patients with psoriasis, an inflammatory skin disease, allows the identification of human-inducible peptide antibiotics, which are absent in healthy skin. With this strategy, the beta-defensins hBD-2 and hBD-3, RNase-7 as well as psoriasin/S100A7 have been discovered as human antimicrobial peptides and proteins. A detailed description of the strategies and methods is presented, which allowed a successful identification and characterization of human antimicrobial peptides. We used various HPLC techniques, combined with antimicrobial testing as read-out system. In parallel, SDS-PAGE analyses as well as electrospray ionization mass spectrometry were used for further biochemical characterization as well as purity assessment. Key words: Antimicrobial peptides, defensin, RNase-7, S100A7, skin, stratum corneum, purification, electrospray ionization mass spectrometry, high-performance liquid chromatography.

1. Introduction Human skin is always in contact with the environment, but despite the presence of many favourable conditions for microbe growth, it is rarely infected. This unexpected observation led to the hypothesis that the uppermost skin layer contains a “chemical defence shield” consisting in antimicrobial peptides. Recent evidence indicates that antimicrobial peptides are synthesized by fully differentiated keratinocytes in the surface-exposed epidermis, a self-renewing stratified squamous epithelium composed of several layers of keratinocytes. Keratinocytes in the outmost A. Giuliani, A.C. Rinaldi (eds.), Antimicrobial Peptides, Methods in Molecular Biology 618, DOI 10.1007/978-1-60761-594-1 2, © Springer Science+Business Media, LLC 2010

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living cells containing layer (stratum granulosum) terminally differentiate and eventually form a physical barrier consisting of the horny layer (stratum corneum, SC). SC cells are sloughed off and replaced by newly differentiated cells originating from epidermal stem cells located in the basal layer. Thus, stratum corneum should be a rich source of human antimicrobial peptides (AMPs) and should allow its detection and characterization in an unbiased approach. Purification of AMPs from skin requires special strategies. First of all, the detection system should be useful for screening to detect the antimicrobial peptide at low concentration. Several assay systems can be used for screening (1), e.g. radial diffusion assay (RDA) or microbroth dilution assay. The RDA assay is a highly sensitive assay which consumes only minimal amounts of peptides for testing (1). Unfortunately the microbroth dilution assay requires approx. 10 times more peptide than the RDA assay (1). Thus, due to the limited availability of human material, the RDA assay might be more useful for successful AMP purification from skin samples. 1.1. Extraction of AMPs from Stratum Corneum

SC is a rich source of various polar and non-polar lipids which make it less efficient to extract peptides and proteins. It might be thus useful to wash the material with a non-polar organic solvent such as ethyl acetate prior to peptide extraction. To achieve an optimal peptide extraction from SC, acidic buffers need to be used. The buffer system should be carefully chosen according to the strategy used for AMP purification: When reversed phase (RP)-HPLC is used as first and sole separation step (when amounts of only a few milligrams of SC are available), SC extraction with acetonitrile containing acidic buffers is recommended. When amounts > 500 mg SC are available, ethanolic citric acid buffers have been proven to be useful for extraction.

1.2. Chromatographic Separation

The SC amounts available will determine the purification strategy. Extracts from a few milligrams of SC will only allow the (partial) purification of the principle AMPs by RP-HPLC. This should be done with a micro-HPLC system. When amounts > 500 mg SC are available, a different, more complex purification protocol, which also includes cation exchange-HPLC, will allow the purification of the principal AMPs as well as most of the less abundant AMPs. Identification of less abundant AMPs requires an enrichment step by pooling the material from different HPLC runs. For enrichment of cationic and amphipatic antimicrobial peptides (which represent by far the majority of all AMPs in SC), heparin-affinity chromatography is useful. The heparin-bound material is then separated by preparative RP-HPLC followed by micro-cation exchange-HPLC and finally micro-RP-HPLC.

Purification of Antimicrobial Peptides from Human Skin

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1.3. Bioassays

Antimicrobial activity in HPLC fractions can be tested with various designer assays (1). HPLC solvents are usually not compatible with the AMP bioassays. In the case of volatile solvents (RPHPLC steps), lyophilization of the samples will be sufficient to get rid of the problem. In the case of cation exchange-HPLC, salts are required for protein elution. Because several AMPs are salt sensitive, there will be a principal risk to get false-negative results. In some cases it is possible to overcome this problem by using unconventional, pragmatic conditions for cation exchange-HPLC using volatile buffers such as ammonia salts at an acidic pH. It is further important to choose the right bacterial target. Many of the AMPs have a restricted activity profile. It is therefore important to use the bacterial target of interest.

1.4. Biochemical Analyses

HPLC fractions should be analysed also by analytical biochemical techniques. Due to the highly cationic behaviour, conventional sodium dodecyl sulphate polyacryl amide electrophoresis (SDSPAGE) analyses often did not work with AMPs. Instead, acidic acryl amide electrophoresis was initially used for checking purity of the AMPs (2). The Tricine–SDS-PAGE system (3) has been now successfully used for determination of the AMP’s size (4–6). It is important to choose electrophoresis conditions which allow sufficient loading of SDS to the highly cationic AMPs and minimize formation of dimers and oligomers. Tricine buffers containing urea were found to be optimal. Due to its high sensitivity, silver staining is preferred for detection of AMPs in the gel, because only nanogram amounts of AMPs are required. RP-HPLC fractions can also be monitored by mass spectrometry. Electrospray ionization mass spectrometry (ESI-MS) is useful to directly determine the exact mass of AMPs in RP-HPLC fractions. Characteristic charge state patterns of AMPs upon ESIMS analyses reveal further structural information about the AMPs isolated from SC. Because ESI-MS is highly sensitive towards the presence of salt, analyses of ion exchange-HPLC fractions requires elimination of anorganic salts, either by the use of volatile buffers or RP cartridges for each separate fraction. HPLC solvents are usually not compatible with the AMP bioassays. In the case of volatile solvents (RP-HPLC steps), lyophilization of the samples will be sufficient to get rid of the problem. In the case of cation exchange-HPLC, salts are required for protein elution. Because several AMPs are salt sensitive, there will be a principal risk to get false-negative results. In some cases it is possible to overcome this problem by using unconventional, pragmatic conditions for cation exchange-HPLC using volatile buffers such as ammonia salts at acidic pH.

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2. Materials 2.1. Extraction of AMPs from SC

1. Suspend stratum corneum or lesional psoriatic scales (e.g. 2.5 g in 100 mL of 0.1 M aqueous citric acid containing 50% (v/v) of 96% ethanol [denaturated with heptane]) (see Note 1). R 2. Homogenizer (Ultraturrax ): use 2,000 rpm for 60 min and chilling in an ice–water mixture.

3. Ultrafiltration: YM3 filters, cutoff of 3 kDa (Millipore, Danvers, MA), are useful (see Note 2). 2.2. Chromatographic Separation of Antimicrobial Peptides

Use HPLC-quality solvents. All chromatographic steps are performed at room temperature (see Note 3). 1. Any HPLC or FPLC machine containing a pump, gradient mixer, UV detector, HPLC columns, and fraction collector can be used. UV detection should be done at either 215, 280 nm, or both. Use solvents that do not show absorbance at 215 nm (e.g. acetonitrile, water, and trifluoroacetic acid [TFA]) (see Note 4). For micro-HPLC we R use a Smart HPLC system (GE Healthcare Biosciences AB, R Uppsala, Sweden) or an ETTAN LC Purifier system (GE Healthcare). 2. For HPLC separation the following columns have been used: a. Heparin Sepharose cartridge (Hi Trap, 10 × 5 mm, 1 mL volume, Amersham) (see Note 5). ˚ reverse phase (RP-8)b. Preparative wide-pore (300 A) HPLC column (C8 Nucleosil with endcapping, 250 × 12.6 mm, 7 mm particle size, Macherey-Nagel, Düren, Germany) (see Note 6). R R -HPLC column for Smart HPLC sysc. Micro-MonoS tem (GE Healthcare) (see Note 7). R d. Micro-RP-18 (C2/C18) column for Smart HPLC system (GE Healthcare) (see Note 8).

2.3. SDS-PAGE Analysis

1. The method of Schägger and von Jagow (3) is used. As sample buffer 50 mM Tris–HCl, 4% (w/v) SDS, 12% (w/v) glycerol, pH 6.8, containing 8 M urea is used (see Note 9). 2. Gels with the dimension 130 × 100 × 1 mm are used and electrophoresis is done in the presence of 8 M urea for 2 h at 10 mA current, 30 V power (power limit 10 W) at room temperature (see Note 10).


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3. Fixation of antimicrobial peptides is done for 30 min with aqueous 2-propanol (30% [v/v]) containing 10% (v/v) acetic acid and 0.3% (v/v) glutaraldehyde (see Note 11). 4. Proteins are stained with 0.03% (w/v) silver nitrate in deionized water followed by developing with a solution of 10% saturated aqueous Na2 CO3 solution containing 0.1% (v/v) of saturated aqueous formaldehyde (40% [v/v]). Development is terminated by acetic acid (3% [w/v] in water) (see Note 12). 2.4. Electrospray Ionization Mass Spectrometry (ESI-MS)

1. We used a Q-TofTM II mass spectrometer (Waters Micromass, Milford, MA). 2. As ESI gas nitrogen was used. 3. Nanoelectrospray ionization was used when sample amounts were limited or for MS/MS peptide sequencing experiments and were carried out after fitting the Q-TofTM II mass spectrometer with a nano-Z spray source (see Note 13). 4. For nanoelectrospray MS analysis nanoflow-electrospray needles (Borosilicate metal-coated glass capillary, Waters Micromass, Milford, MA) were used. Salt containing samples are desalted using self-prepared ␮-columns using constricted GelLoader tips (Eppendorf, Wesseling-Berzdorf, R Germany) packed with a 2:1 mixture of Poros 50R2 and Oligo R3 reversed phase medium (Applied Biosystems, Forster City, CA). 5. Acquisition and data analysis are performed using the MassLynx 4 software package supplied by Waters Micromass, Milford, MA.

2.5. Antimicrobial Activity Assay

The radial diffusion assay was used according to Steinberg and Lehrer (1) (see Note 14). 1. Trypticase soy broth (TSB, Difco, Detroit, MI): Full strength broth (30 g per litre deionized water), autoclaved, and stored at room temperature. 2. Sterile phosphate buffer, pH 7.4 or 6.5 (or as desired). 3. Agarose (Sigma): The use of a low electroendosmosis (EEO)-type agarose in place of standard agar is critical to limit electrostatic interactions between cationic AMPs and sulphated moieties of the agaropectin component of standard agar (1). 4. Underlay gels (1): Mix 50 mL of 100 mM sodium phosphate buffer with 5 mL full-strength trypticase soy broth, add 5 g agarose, and bring the volume to 500 mL with deionized distilled water. Adjust the final pH with NaOH or HCl, place the suspension on a hot plate, and stir it under heat until the

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agarose dissolves. Dispense 50-mL aliquots, autoclave them at 121◦ C for 20 min, and store the sterilized media at room temperature. Before use, the solidified medium should be fluidized (we use a microwave oven) and placed it into a water bath maintained at 42◦ C. 5. Overlay agar (1): This agar contains 60 g (twice the customary amount) of trypticase soy broth (TSB, Difco) and 10 g agarose (Sigma) per litre of deionized water and is similarly treated as the underlay gels. 6. Microorganisms: Escherichia coli, Staphylococcus aureus, and Candida albicans were used for routine AMP testing after determination of optical density (OD)/colony forming unit (CFU) ratio (see Note 15). 7. Peptides are introduced into 3 mm sample wells within the underlay gel.

3. Methods 3.1. Extraction of AMPs from Stratum Corneum

1. Wash 1 g heel stratum corneum (SC) with 50 mL ethylacetate and dry it under vacuum (see Note 16). 2. Suspend SC in acidic buffer, homogenize, and then add ethanol (see Note 17). 3. Centrifuge and use supernatant (see Note 18). 4. Concentrate the supernatant to ∼ 5–10 mL, adjust to pH 8.0, then again to pH 4–4.5, centrifuge it again, and freeze it (at –20◦ C) until further use (see Note 19). 5. For further purification, thaw the sample, adjust the pH to pH 8.0, centrifuge it, and apply it to a heparin affinity column (see Note 20). 6. Wash the column with 3 volumes of equilibration buffer: 10 mM Tris–citrate, pH 8.0. 7. Strip the bound material from the column by the use of 3 mL 2 M NaCl in equilibration buffer (see Note 21). 8. Add trifluoroacetic acid (TFA) and adjust to pH 3.

3.2. Preparative RP-8-HPLC

1. Apply the heparin-bound material (from Section 3.1, Step 8.) to a preparative RP-8-HPLC column by the use of a 2–5 mL loop (see Note 22). 2. Separate proteins by elution with a gradient of increasing concentrations of acetonitrile. Turn the detector on 215 nm and – when possible also 280 nm – and choose the integrator


21

attenuation appropriate to protein amounts you expect (see Note 23). 3. Separate peaks – when possible – manually according to the appearance of UV-absorbing peaks and shoulders (see Note 24). 4. Place fractions immediately in the refrigerator. 5. Take off an aliquot of each fraction for the bioassay, SDSPAGE analysis, or ESI-MS analyses using a microtitre plate (see Note 25). 3.3. Micro-MonoSR Cation Exchange HPLC

1. Combine fractions of RP-8-HPLC, which contain the same AMP and lyophilize them. 2. Dissolve the residue in 50–200 ␮L 20 mM ammonium formate buffer, pH 4.0, which contains 25% (v/v) acetonitrile. R 3. Apply the sample to a micro-MonoS -HPLC column, which has been equilibrated with the same acetonitrilecontaining ammonium formate buffer, pH 4.0 (see Note 26).

4. Elute with a gradient (0–20 min) of increasing concentrations of NaCl (0–1 M) (see Note 27). 5. Take off an aliquot of each fraction for the bioassay, SDSPAGE analysis, or ESI-MS analyses using a microtitre plate (see Note 25). 3.4. Micropore C2/C18-RP-HPLC

1. Combine fractions containing the same AMP and apply them directly onto a micropore C2/C18-RP-HPLC column (see Note 28). 2. Elute proteins with increasing concentrations of acetonitrile. Turn the UV detector on 215 nm (and 280 nm, if possible) and separate peaks manually. 3. Take off an aliquot of each fraction for the bioassay, SDSPAGE analysis, or ESI-MS analyses using a microtitre plate (see Note 25).

3.5. Radial Diffusion Antimicrobial Activity Assay

1. Prepare organisms for the assay as well as the gel as outlined in Section 2.5. 2. Add 30 ␮L aliquots of preparative RP-8-HPLC fractions or 2 ␮L aliquots of micro-HPLC fractions to the wells of a round-bottom well microtitre plate. Lyophilize samples and add to each well 8 ␮L 0.01% (v/v) aqueous acetic acid and transfer 5 ␮L aliquots of the various samples into each well in the underlay gel. 3. Incubate the gel for 3 h in a 37◦ C incubator, then add the overlay, and incubate at 37◦ C overnight.

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4. Calculate the results by measuring the diameter of the clearing zone (see Note 29). 3.6. SDS-PAGE Analyses

1. Mix fractions (30 ␮L of RP8-HPLC fractions, 2 ␮L R of MonoS -HPLC, and C2/C18-micro-HPLC fractions) with 10 ␮L sample buffer and boil for 10 min (see Note 30). Then load sample on the stacking gel and separate electrophoretically in the presence of 8 M urea (30 min at 100 V, 400 mA; then 90 min at 120 V, 400 mA) (see Note 31). 2. Fix peptides in the gel with fixation solution. 3. Stain proteins with silver nitrate solution (see Note 32).

3.7. Electrospray Ionization Mass Spectrometry (ESI-MS) Analyses

1. For routine MS analysis, dilute aliquots (2–10 ␮L) of HPLC fractions containing the sample with 100 ␮L carrier solvent (50:50 acetonitrile:water containing 0.2% (v/v) formic acid) and infuse it into the electrospray source at a rate of 10–20 ␮L/min (see Note 33). Sodium iodide can be used for mass calibration for a calibration range of m/z 100–2,000. The capillary potential is set to 3.5 or 4 kV and cone voltages between 25 and 75 V are chosen; cone temperature is set to 80◦ C; desolvation temperature is 150◦ C. The charge-tomass ratio of ions is scanned within the range of 280–2,000. 2. For nanoelectrospray MS analysis a 1–3 ␮L aliquot of saltfree sample (see Note 34) is loaded into the nanoflowelectrospray needle. Salt containing samples are desalted using self-prepared ␮-columns. Formic acid is added to the samples just before desalting to give a final concentration of 5% (v/v). After loading the column with the sample the column should be washed two times with 10 ␮L 5% formic acid. Peptides are eluted with 1–3 ␮L 60% methanol/5% formic acid directly into the nanoelectrospray needle and measured by nanoelectrospray ionization MS using a capillary voltage between 1 and 1.4 kV. 3. For mass mapping (mass fingerprint) when necessary, cysteine residues are reduced (by incubation of HPLC fractions containing 10–20 ␮g protein in 85 ␮L 100 mM NH4 HCO3 , 10 mM dithiothreitol (DTT) for 20 min at 60◦ C) and subsequently alkylated (by incubation in 200 mM iodoacetamide for 20 min at RT) in the dark. Prior to digesR tion samples are desalted using 10 ␮L C18 Poros pipette tips or HPLC with C2 /C18 columns. HPLC sample fractions are either directly or after reduction and alkylation of cysteine residues subjected to trypsin digestion: lyophilized samples containing 2–4 ␮g protein are dissolved in 20 ␮L 100 mM NH4 HCO3 , pH 8; tryptic digestion is started by adding 50 ng (with 1% acetic acid)


23

activated trypsin (modified trypsin, sequencing grade, Roche; 1:50 final molar enzyme:substrate ratio) and is allowed to proceed for at least 4 h at 37◦ C. Digests are either analysed directly or stored frozen until subsequent mass mapping: tryptic fragment masses are determined after desalting using self-prepared ␮-columns (Section 2.5, Step 4) using ESI-MS. 4. Peptide sequencing by MS/MS is done by analyses of tryptic peptide fragments using a Q-TOF 2 mass spectrometer (Waters Micromass, Milford, MA) with nanoelectrospray ionization (see Note 35). Cone voltage and collision energy used to perform MS–MS are optimized for each peptide analysed. Collision energy varied between 17 and 40 eV with argon (14 psi) as the collision gas. Data for MS/MS are acquired over the mass range m/z 80–2,000. 5. Mass spectra are averaged typically over 2–10 scans (20– 2 s/scan). The multiply charged raw data of intact proteins are background-subtracted and deconvoluted using MaxEnt1 to obtain singly charged ion mass spectra to determine average molecular masses of intact proteins. The raw combined spectral data from small peptides or tryptic protein fragments or obtained after MS/MS fragmentation of selected precursor ions are background subtracted and subjected to Maximum Entropy 3 (“MaxEnt3”) deconvolution to determine monoisotopic molecular masses. Sample identity is determined by database search analysis of peptide fragment mass patterns and/or after de novo sequencing of tryptic peptide fragments. All mass fingerprint and MS/MS data are searched against the human protein database using the Mascot program (Matrix Science, Boston, MA). Peptide sequences are directly (“de novo”) determined from MS/MS data using the software program PepSeq from the MassLynx4 software package (Waters Micromass, Milford, MA). PepSeq-derived peptide sequences are analysed with the NCBI-BLAST protein database search program.

4. Notes 1. Heptane-denaturated ethanol is cheaper than nondenaturated ethanol. Highly volatile heptane does not interfere with any purification step. Instead of ethanol, acetonitrile can also be used. In the absence of organic solvents we were confronted with severe problems with the extracts, which gave turbid solutions after centrifugation

24

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with a high content of fines (lipid drops mixed with solid particles). Ignoring this phenomenon has usually resulted in HPLC problems, such as high-pressure error and giving “memory compounds” on the HPLC column (7). Protease inhibitor cocktails have not been added to the stratum corneum prior to extraction. We never observed proteolytic digests of the AMPs which we had isolated so far from stratum corneum. This includes hBD-2, hBD-3, RNase-7 (4–6), and psoriasin (8). In particular RNase-7 and psoriasin are extremely sensitive towards proteolysis. We therefore speculate that in skin endogenous protease inhibitors prevent proteolysis of AMPs. 2. The recovery of AMPs using Amicon (Danvess, MA) filters was found to be highest when acidic solutions containing a small percentage (20–30%) of water-soluble organic solvents were used. Use the right diameter of the filter to avoid losses of AMPs due to an un-appropriate ratio of filter diameter and (final) sample volume. Small extract volumes (100 ␮L–1 mL) should be better either lyophilized or concentrated by vacuum evaporation or directly applied to the RP-HPLC column for separation. Losses of material seen in some cases usually come from sticking to the surfaces rather than degradation. Once cationic AMPs sticked to surfaces (glass, siliconized glass, plastic), we have been unable to reverse the process by washing with organic solvents. Therefore, our strategy to avoid sticking is to add organic solvents whenever possible at acidic pH to AMPcontaining solutions. 3. It is our experience that chromatography at low temperature is not necessary for AMP purification. Skin-derived AMPs are remarkably stable at ambient temperature. 4. UV detection at 215 nm allows quantification of protein content and thus estimation of the AMP amounts in purified peaks. Although we used ubiquitin for calibration, the absolute amounts of known AMPs can be estimated from its calculated extinction coefficient. 5. For extracts from >10 g stratum corneum a 5 mL heparin– sepharose cartridge is recommended. 6. A wide variety of reverse-phase columns obtained from different manufacturers can be used. Take care to use wide ˚ columns with endcapping. Most of the AMPs pore (300 A) are very cationic. When there is no endcapping (which blocks the free silanol groups of the silica bead material), the highly cationic AMPs will show broadened peaks and often dramatic losses of recovery are observed. Choose RPHPLC columns which have been optimized for the separation of basic compounds.


25

7. Do not use oversized cation exchange columns! For extracts obtained from >1 g stratum corneum we use the R micro-MonoS -HPLC column. For smaller amounts we R are using a MiniS -HPLC column. 8. C2/C18-␮HPLC columns give excellent resolution for several AMPs. When only little stratum corneum material is available and a single HPLC analysis is possible, a (micro)column with this material is recommended. In our hands classical wide pore C8-RP columns do not always allow complete separation of lysozyme from hBD-2. The use of a ␮C2/C18 column leads to a retention time difference of about 10 min! 9. Addition of urea is essential for several AMPs to get bands at the expected size in the gel. For example, hBD-2 shows R in “Phast -System-high density gels”, which lack urea, a 14 kDa band, just below that of lysozyme, whereas in Tricine gels with urea a band at 4 kDa can be observed. 10. With this method we obtained highest resolution of bands. We were able to separate the different 77, 72, and 69 residues containing forms of interleukin-8 (9). 11. Fixation can be a problem for low MW AMPs. The use of glutaraldehyde is compelling for detection of low amounts (< 10 ng per lane) of AMPs. 12. When highly sensitive detection is necessary, the gels can be destained with K3 [Fe (CN)6 ] until background is cleared. Bands should never be completely destained! After rinsing the destaining solution, staining can be repeated as described. The band intensity does not reflect the relative amounts of the applied proteins. 13. Nanospray modus is recommended when very low peptide amounts are available. RP-HPLC fractions should be lyophilized and the (invisible) residue dissolved in 5 ␮L ESI-MS solvent (see Section 3.7, Item 1). It is essential to completely evaporate the HPLC solvent, because otherwise remaining TFA will affect sensitivity. Take care to avoid the presence of detergents, which make analyses impossible. 14. This assay is highly sensitive and needs only minimal amounts of the preparation being tested. With appropriate solvent controls it is possible to test micro-HPLC fractions without any lyophilization. In some cases it could be necessary to protect HPLC fractions from losses by irreversible adherence to the plate. When this is a problem, add 5 ␮L 0.1% (w/v) bovine serum albumin in 0.01% aqueous acetic acid to each well of the microtitre plate prior to adding HPLC fractions.

26

¨ Schroder

15. Vigorous mixing of bacterial suspensions (especially for Pseudomonas aeruginosa and after centrifugation) is important to disperse any clumps and provide an even inoculum suspension (1). 16. It is our experience that ethylacetate treatment of stratum corneum enhances recovery of AMPs, possibly by dissolving non-polar lipids and therefore increasing access of aqueous solutions to stratum corneum particles, which contain high amounts of lipids. Treatment with acetone is not recommended because most of the AMPs are soluble in acetone and thus would be lost. Alternatively diethylether could be used, but this requires extreme care! 17. Instead of ethanol, acetonitrile can also be used. In the absence of organic solvents, we often have had problems with the extracts giving turbid solutions after centrifugation with a high content of fines (lipid drops mixed with solid particles). Ignoring this phenomenon has usually resulted in HPLC problems, such as high-pressure error and giving “memory compounds” on the HPLC column. 18. The recovery of AMPs using Amicon (Danvess, MA) filters was found to be highest when acidic (pH < 3) solutions containing a small percentage (20–30%) of water-soluble organic solvents were used. Use the right diameter of the filter to avoid losses due to inappropriate ratio of filter diameter and (final) sample volume. 19. pH adjustment to pH 8 has always been done after thawing of frozen acidic samples. It is our experience that AMP recovery from samples which have been stored at pH 8 were always lower than those stored at acidic pH. After adjustment of extracts to an acidic pH often very fine precipitates occur. It is recommended to centrifuge these concentrated extracts again to avoid problems with HPLC analyses. 20. The size of the heparin affinity cartridge should be appropriate to the amount of extracted material. For extracts obtained from stratum corneum amounts < 1 g we always used a 1 mL cartridge. A 5 mL cartridge was used for higher amounts of extracts. It could be important to perform a second heparin affinity chromatography to see whether the whole heparin-binding material was indeed bound in the first chromatography step. Initially we had diafiltered the extracts to omit low MW compounds. Today we directly apply the extracts onto the heparin column. If extracts are directly (without diafiltration) applied, be aware that also low MW cationic compounds (which could represent antibiotic substances) will bind to the heparin


27

column! If your antimicrobially active HPLC fractions do not show strong silver stained bands and no masses > 2 kDa upon ESI-MS, look for the raw data (single charged species) of the ESI-MS analyses to identify possibly a low MW antibiotic compound! 21. It may occur that not all AMPs are efficiently stripped from the column with 2 M NaCl. We have observed that most of the hBD-3 and parts of HNP-1 sticked to the heparin column. hBD-3 could be eluted with acidic buffers like 0.1 M glycine/HCl buffer, pH 2 and HNP-1 with 0.1 M NaOH. Be aware that a repeated use of these eluents may destroy AMP-binding capacities of the heparin columns when often re-used! 22. Instead of concentrating the samples to a very low volume we used injection loops with the capacity for several millilitre sample volume. Broadening of peaks was never found to be a problem, except when the samples contained organic solvents >10%. When very polar AMPs are expected, it is recommended to lyophilize or “SpeedVac” the (acidic) sample and dissolve the residue in a small volume of water. 23. Detection at 215 nm is recommended, because some of the AMPs show no or a very low absorbance at 280 nm. When possible, absorbance at three wavelengths (215, 254, 280 nm) should be measured because the absorbance ratio is very characteristic for each peptide. This UV absorbance profile together with the retention time will often give sufficient initial information about the AMP that eluted in given HPLC fractions. 24. We use manual separation of HPLC fractions. Often AMPs do not represent the major UV-absorbing peaks, but instead shoulders within the peak. These can be easily separated manually and then analysed for its specific AMP activity. If this is higher in the shoulder than in the major UVabsorbing peak, it indicates that most of the contaminating protein has already been separated. It is important for a successful purification of AMPs to separate as early as possible contaminating non-active impurities. 25. We take, just after the RP-HPLC step, aliquots of each HPLC fraction and place it into round-bottomed microtitre plates (for each assay system one plate to avoid repeated freezing and thawing), which then will be stored frozen (–20◦ C). Immediately before biological testing will be performed, samples are lyophilized and then dissolved in appropriate solvents.

28

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26. We use unusual conditions for cation exchange-HPLC for AMP separation! These conditions were found to be optimal for separation of various skin proteins (4–8) and allowed us good recoveries of highly cationic AMPs. It is our experience that textbook conditions (neutral pH, anionic buffers) gave lower AMP resolution (broad peaks!) and lower recoveries. Highly cationic AMPs, which are eluting only with high NaCl content, often cannot be detected in antibacterial assay systems due to AMP’s salt sensitivity. Therefore, it has been sometimes our strategy to separate all, at high NaCl eluting proteins by subsequent (C2/C18)-RP-HPLC and to test RP-HPLC fractions for AMP activity. 27. Instead of acetonitrile also 30% (v/v) ethanol (denaturated with heptane) can be used. Addition of organic solvents to the elution buffer is essential for high AMP recovery. It is believed that amphipathic AMPs otherwise stick to the cation-exchanger matrix. 28. Fractions need not to be concentrated to decrease the volume, when an injection loop of appropriate size is available. It is recommended to add 1 ␮L TFA/1 mL fraction. 29. Depending on the peptide, sometimes a completely clear zone, a clear zone with bacterial growth within the clearing zone or a complete clear zone, which is surrounded by a concentric zone of partial clearing owing to a reduction in microcolony density, was observed. We found the different patterns as AMP-specific parameters, which also depended on the concentration of the AMP as well as the assay condition, including the test organism. 30. We always performed SDS-PAGE analyses in the absence of reducing agents, because we never saw better band resolution in its presence. In contrast, some AMPs showed broader bands in the presence of dithiothreitol or mercaptoethanol. 31. Urea is necessary to reduce or prevent formation of dimers and oligomeric peptides. HBD-2 (MW ∼ 4 kDa) migrates in the absence of urea like a 16 kDa protein. HBD-3 (MW ∼ 5 kDa) still migrates in the presence of urea like a 9 kDa peptide. 32. Note a different band shape (even, convex, or concave) and band staining colours of different AMPs, e.g. defensins always showed a grey colour, whereas psoriasin and lysozyme were stained red-brown. 33. Take care that samples do not contain too much TFA, which would cause low signal intensity. It may be helpful to lyophilize (or “SpeedVac”) the sample prior to


29

ESI-MS analyses and dissolve it in ESI-MS solvent. SamR -HPLC cannot be measured ples originating from MonoS directly upon ESI-MS (due to the salt content). Intensive signals of anorganic salt clusters do not allow detection of far less intensive protein signals. NaCl-containing cation exchange-HPLC fractions therefore require a desalting process, otherwise no protein signals are visible. Alternatively, cation exchange-HPLC can be performed with volatile buffers (e.g. 1 M ammonium formate) as eluents. When adducts of ammonium formate adducts are still observed, we recommend to repeatedly add water to the samples and repeatedly lyophilize them until no crystalline residue (from salt) is visible. 34. Nano-ESI-MS is recommended when only low AMP amounts are expected. Because for nanospray-ESI-MS analyses only a few microlitres are required, due to the high TFA content it is essential to lyophilize the HPLC fractions prior to analyses! Dissolve the residue in sample solvent. 35. Peptide digests should be passed through a self-prepared ␮column and then eluted with acetonitrile. This procedure gives far less background and therefore much better results than the direct application of digests due to enrichment as well as elimination of contaminants.

Acknowledgments This work was supported by Deutsche Forschungsgemeinschaft, SFB 617.

References 1. Steinberg, D. A. and Lehrer, R. I. (1997) Designer assays for antimicrobial peptides. Disputing the “one-sizefits-all” theory. Methods Mol. Biol. 78(1), 69–186. 2. Ganz, T., Metcalf, J. A., Gallin, J. I., Boxer, L. A., and Lehrer, R. I. (1988) Microbicidal/cytotoxic proteins of neutrophils are deficient in two disorders: Chediak-Higashi syndrome and “specific” granule deficiency. J Clin. Invest. 82, 552–556. 3. Schägger, H. and von Jagow, G. (1987) Tricine-sodium dodecyl sulfatepolyacrylamide gel electrophoresis for the

separation of proteins in the range from 1 to 100 kDa. Anal. Biochem. 166, 368–379. 4. Harder, J., Bartels, J., Christophers, E., and Schröder, J. M. (1997) A peptide antibiotic from human skin. Nature 387, 861. 5. Harder, J., Bartels, J., Christophers, E., and Schröder, J. M. (2001) Isolation and characterization of human beta -defensin-3, a novel human inducible peptide antibiotic. J. Biol. Chem. 276, 5707–5713. 6. Harder, J. and Schröder, J. M. (2002) RNase 7, a novel innate immune defense antimicrobial protein of healthy human skin. J. Biol. Chem. 277, 46779–46784.

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7. Schröder, J. M. (2000) Purification of chemokines from natural sources. Methods Mol. Biol. 138, 1–10. 8. Gläser, R., Harder, J., Lange, H., Bartels, J., Christophers, E., and Schröder, J. M. (2005) Antimicrobial psoriasin (S100A7) protects human skin from Escherichia coli infection. Nat. Immunol. 6, 57–64.

9. Schröder, J. M., Mrowietz, U., Morita, E., and Christophers, E. (1987) Purification and partial biochemical characterization of a human monocyte-derived, neutrophil-activating peptide that lacks interleukin 1 activity. J. Immunol. 139, 3474–3483.

Chapter 3 Strategies for the Isolation and Characterization of Antibacterial Lantibiotics Daniela Jabes and Stefano Donadio Abstract Lantibiotics are biologically active peptides produced by several strains from the phyla Firmicutes and Actinobacteria. They are ribosomally synthesized and undergo posttranslational modifications that endow them with the characteristic (methyl)-lanthionine residues. As a result, lantibiotics contain a variable number of rings, each carrying one thioether link. Many lantibiotics inhibit growth of Gram-positive bacterial strains by interfering with peptidoglycan formation. Because they bind to the key intermediate lipid II at a site not affected by clinically used antibiotics, they are effective against multidrug-resistant strains. We describe a bioassay-based method suitable for finding antibacterial lantibiotics from actinomycete strains and provide selected procedures for characterizing newly discovered lantibiotics for their antibacterial properties. Key words: Actinomycetes, antibiotics, bioactive peptides, lantibiotics, MRSA, screening.

1. Introduction 1.1. Definition of Lantibiotics

The term lantibiotics refers to a family of ribosomally synthesized, posttranslationally modified peptides, which are characterized by the presence of (methyl)-lanthionine residues (1, 2). These amino acids (Fig. 3.1) result from the formation of thioether bridges between cysteine thiols and dehydroalanine or dehydrobutyrine residues, which in turn derive from dehydration of serine and threonine, respectively. These thioether bridges impart conformational constraints to these molecules generating a series of rings (usually numbered in alphabetical order), which are essential for biological activity. In addition to these features,

A. Giuliani, A.C. Rinaldi (eds.), Antimicrobial Peptides, Methods in Molecular Biology 618, DOI 10.1007/978-1-60761-594-1 3, © Springer Science+Business Media, LLC 2010

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Fig. 3.1. Structure of lanthionine (X=H) and of methyl-lanthionine (X=CH3 ) and their schematic representations (bottom) in lantibiotics.

lantibiotics may contain other posttranslational modifications (1, 2). Within the lantibiotics discovered so far, modifications may include 2,3-dehydroalanine (Dha) and (Z)-2,3-dehydrobutyrine (Dhb), derived from serine and threonine residues, respectively, not recruited in thioether bridges; a C-terminal S-aminovinylD -cysteine (or its 3-methyl analog), derived from decarboxylation and cross-linkage of the C-terminal cysteine residue; N-terminal oxopropionyl and 2-oxobutyryl, resulting from spontaneous dehydration of N-terminal Dha and Dhb residues; a lysinoalanine bridge; hydroxylated aspartic acid or proline residues; or a chlorinated tryptophan residue. Lantibiotics are produced by Gram-positive bacteria and have been reported so far only from the phyla Firmicutes and Actinobacteria. It should be noted that most lantibiotics were identified using bioactivity-based screens for antibacterial activity. The recent discovery that lantibiotics participate in morphological development in Streptomyces spp. (2) suggests that additional biological activities may be uncovered within this class. Similarly, inspection of the increasing number of microbial genomes for genes typical of lantibiotic biosynthesis may lead to the identification of additional lantibiotics in a bioassay-independent manner. 1.2. Biological Activity of Lantibiotics

Although the great majority of known lantibiotics have antimicrobial activity, this might be a consequence of the assays used to discover them. Indeed, some compounds display other bioactivities, including potentially interesting pharmacological properties. For example, cinnamycin (Fig. 3.2) and the related duramycins are

Strategies for the Isolation and Characterization of Antibacterial Lantibiotics

33

Fig. 3.2. Some lantibiotics mentioned in the text.

potent inhibitors of phospholipase A2 (3). Moreover, duramycin has been shown to increase chloride secretion in lung epithelium (4) and has been in clinical trials to evaluate its efficacy in clearing mucus secretions associated with cystic fibrosis and other airway diseases (5). Another example is cytolysin that, in addition to having antimicrobial activity, functions as a virulence factor, lysing erythrocytes and polymorphonuclear leukocytes (6). Finally, the peptides SapB and SapT, produced by the filamentous soil microbes Streptomyces coelicolor and S. tendae, respectively (7, 8), are hydrophobic, surface-active compounds believed to function as biosurfactants, releasing the surface tension at the colony–air interface to facilitate the emergence of nascent aerial hyphae (9). 1.3. Mode of Action of Antibacterial Lantibiotics

Traditionally, lantibiotics possessing antibacterial activity have been classified into two subgroups: type-A lantibiotics, exemplified by nisin (Fig. 3.2), are elongated, amphiphilic peptides; while type-B lantibiotics, exemplified by mersacidin (Fig. 3.2), are compact and globular (10). More recently, a biogenetic classification has been proposed for antibacterial lantibiotics, which places them in either class I or class II on the basis of the pathway by which maturation of the peptide occurs (2, 11). [A class III has also been proposed for the morphogenic lantibiotics, which probably require a different pathway for peptide maturation (2).]

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This designation is less dependent on the structure of the mature lantibiotic and can accommodate, for example, globular-type lantibiotics such as NAI-107 (also known as 107891) and 97518 (Fig. 3.2), which share nonetheless the same pharmacophore as nisin (12, 13). Despite differences in shape and primary structure, both nisin- and mersacidin-type lantibiotics interact with the membrane-bound peptidoglycan precursor lipid II. However, binding to this essential intermediate in peptidoglycan biosynthesis involves different portions in the two classes of lantibiotics, and further events may occur after it. For example, it has been demonstrated that the two N-terminal rings of nisin dock on lipid II, followed by oligomerization of the resulting complex after membrane insertion of the C-terminal portion of the lantibiotic. In contrast, globular lantibiotics such as mersacidin are incapable of forming pores. 1.4. Biosynthesis of Lantibiotics

Lantibiotics are synthesized ribosomally from a pre-propeptide, often designated with the generic name LanA, which consists of a leader peptide preceding the structural segment (the propeptide). The propeptide undergoes the modifications required for lantibiotic maturation, while the leader peptide acts as a recognition sequence for the lantibiotic processing enzymes and is eventually removed from the mature lantibiotic (1, 2). Serine and threonine residues in the propeptide are dehydrated to Dha and Dhb, respectively. Subsequent intramolecular Michael-type addition by cysteine thiols to the unsaturated side chains yields the corresponding thioethers (Fig. 3.3). In class I lantibiotics, the dehydration and cyclization steps are catalyzed by two distinct enzymes, designated LanB and LanC, respectively, whereas a bifunctional LanM enzyme is responsible for both reactions in class II lantibiotics. Further posttranslational modifications may also occur during or after thioether formation. Eventually, the leader peptide is removed to produce the mature lantibiotic. For most lantibiotics, the ABC-type transporter LanT transports the modified peptides out of the cytoplasm.

Fig. 3.3. Formation of lanthionines.

1.5. Scope

This chapter describes detailed procedures for the discovery of antibacterial lantibiotics and for the evaluation of their potential as antibiotics. Recent advances in the in vitro and in vivo manipulation of lantibiotic biosynthesis provide effective tools for


35

generating variants of existing lantibiotic classes. The reader is referred to recent publications on how to employ lantibiotic biosynthesis enzymes for generating new variants (14) or on the genetic manipulation of lantibiotic producer strains (15).

2. Materials 2.1. Bacterial Strains

1. The microbial strains used in this work derive from the NAICONS strain collection. For the screening test to detect lantibiotics, the strains used were S. aureus ATCC 6538P and its L-form, prepared as described (16). The other strains described here and their relevant phenotypes are reported in Tables 3.1 and 3.2. However, strains equivalent to those described here can be obtained from public collections.

Table 3.1 An initial panel of bacterial strains for evaluating lantibiotics Medium

Strain

MHB

Staphylococcus aureus MSSA 6538P

MHB

Staphylococcus aureus MetR 1400

THB

Streptococcus pyogenes

THB

Streptococcus pneumoniae P203

MHB

Streptococcus haemolyticus

MHB

Listeria monocytogenes ATCC 4428

MHB

Enterococcus faecium VanS

MHB

Enterococcus faecium VanA

MHB

Enterococcus faecalis VanS

MHB

Enterococcus faecalis VanA

MHB

Escherichia coli K12

7H9

Mycobacterium smegmatis mcG 155

Frozen stocks are prepared by collecting mid-exponential cultures in the appropriate medium, adding glycerol to 20% (v/v), and dispensing the cultures as small aliquots in different vials. After freezing, one vial is thawed and used for the determination of colony-forming units (CFU). Strains can be maintained at –80◦ C for prolonged periods of time. 2.2. Media

The media described here were all from Difco, unless otherwise specified, and were prepared according to the manufacturer’s instructions:

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Table 3.2 Suggested strains, media, and culture conditions for further characterization of lantibiotics Strain

Culture medium

Incubation

Neisseria meningitidis ATCC 13090 ATCC

Supplemented GCB

35◦ C, 24 h, 5% CO2

Haemophilus influenzae 19418

HTM

35◦ C, 24 h

Moraxella catarrhalis ATCC 8176

MHB

35◦ C, 24 h

Corynebacterium diphtheriae

MHB

35◦ C, 24 h

Propionibacterium acnes

BB

Clostridium difficile

Oxyrase-supplemented WCB

35◦ C, 24 h, anaerobic atmosphere 35◦ C, 24 h, anaerobic atmosphere

Lactobacillus spp.

LB

35◦ C, 24 h

Bacillus subtilis

AM 3

35◦ C, 24 h

1. Brain Heart Infusion (BHI). 2. Cation-adjusted Mueller Hinton Broth (MHB), with CaCl2 and MgCl2 to final concentrations of 20 and 10 mg/L, respectively. 3. Mueller Hinton Agar (MHA). 4. Todd Hewitt Broth (THB). 5. MHSA is MHB containing 0.7% agar. 6. Middlebrook 7H9 Broth (7H9), supplemented with 10% oleic acid–albumin–dextrose catalase (Beckton Dickinson) and 0.2% glycerol. 7. Gonococcus-Supplemented Broth (GCB), supplemented with 1% isovitalex (Beckton Dickinson) and 5 mg/L hemin solution (Sigma). 8. Haemophilus Test Medium (HTM); Brucella Broth (BB) supplemented with 5 mg/L hemin, 1 mg/L vitamin K1 , and 5% lysed horse blood (Oxoid). 9. Wilkins–Chalgren Broth (WCB) supplemented with 1:25 v/v oxyrase (Oxyrase Inc.). 10. Lactobacillus Broth (LB). 11. Antibiotic Medium 3 (AM3).

2.3. Other Chemicals

1. All antibiotics used for determination of minimal inhibitory concentration (MIC) are dissolved in DMSO to obtain


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stock solutions of 10 mg/mL. Then, they are appropriately diluted with the specific growth medium to obtain working solutions, from which serial 1:2 dilutions are performed. 2. Bovine serum albumin (BSA) for well coating is prepared as a 0.02% solution in distilled water, filter sterilized, and kept at 4◦ C for up to 1 week. 3. Human serum (Sigma Chemical) is filter sterilized and kept at 4◦ C for up to 1 week. 4. The ␤-lactamase mixture consists of 0.001 and 0.002 U/mL type-1 and type-2 penicillinases, respectively, from Bacillus cereus; and 0.0025 and 0.5 U/mL type-3 and type-4 penicillinases from Enterobacter cloacae. All enzymes were purchased from Sigma.

3. Methods 3.1. Identification of Antibacterial Lantibiotics

Genomic-based approaches for discovering lantibiotic gene clusters have been described and will not be mentioned here (14). We will focus on the use of a bioassay that, according to our experience, resulted in a high frequency of lantibiotics among fermentation broth extracts derived from different actinomycete genera. Indeed, when this screening program was applied to a library of ca. 120,000 extracts, lantibiotics represented over 60% of observed hits. It remains to be determined whether this high percentage resulted from biases in the type of strains (e.g., a relatively low percentage of Streptomyces spp. and a high incidence of Actinoplanes spp.) or in the over-representation of samples derived from just a few lantibiotic-producing strains. In any case, others have observed the relative abundance of lantibiotics among actinomycetes (17). The following procedure describes a series of four tests in a bioassay-based screening for discovering cell-wallacting lantibiotics from microbial fermentation extracts. Extracts can be prepared by different methods, provided that care is taken to ensure sufficient diversity of the strains from which fermentation extracts are derived (18). 1. Dispense 10 ␮L aliquots of samples to be tested in each well of a 96-well microtiter plate for a total of 80 samples, leaving the remaining wells for positive and negative controls (see Note 1). 2. Prepare the inoculum by dispensing an appropriate amount of the frozen S. aureus ATCC 6538P stock into BHI medium to obtain a final titer of approximately 105 CFU/mL. 3. Add 90 ␮L of the bacterial inoculum to each well of the microtiter plate from Step 1 and incubate for 24 h at 35◦ C.

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4. Measure the turbidity of each well at 590 nm in a suitable multiplate reader (e.g., Tecan SpectraFluor) and express results as Ii = 100 × [1 − (Ti − Tc )/(Tp − Tc )], where Ii is the percent growth inhibition of sample i, with Ti representing the absorbance values of sample i, and Tc and Tp the averages of negative and positive controls, respectively. 5. Identify those samples showing an Ii value ≥90 in Step 4 (see Note 2). 6. Prepare two identical plates, each containing 10 ␮L aliquots of 10 different positives in the upper row, and serial 1:2 dilutions of each sample in the remaining rows. 7. Use one plate to repeat Steps 2–4, determining for each sample and its dilutions the corresponding Ii . 8. Prepare the L-form inoculum, by diluting 1:2 an overnight culture in BHI with fresh medium, and add 90 ␮L per well to the second plate from Step 6. Use positive and negative controls in the remaining wells (see Note 3). Incubate at 35◦ C for 24 h. 9. For each sample and its dilutions from Step 8, measure absorbance as in Step 4, expressing results as G i = 100 × [1 − (Ai − Ac )/(Ap − Ac )], where Gi is the percent growth inhibition of sample i, with Ai representing the absorbance values of sample i, and Ac and Ap the averages of negative and positive controls, respectively. 10. Determine for each sample DI and DG , i.e., the highest dilutions giving I and G values ≥80 and ≤40, respectively (see Note 4). 11. Identify those samples showing an I value ≥80 and a DI /DG ratio ≥8 in Step 10 (see Note 5). 12. Prepare two new sets of identical plates, each containing 10 ␮L aliquots of different positives. 13. To one plate from Step 12, add 10 ␮L of the mixture of penicillinases and incubate for 1 h at 37◦ C, before adding the S. aureus inoculum and incubating as in Step 3. Record Ii values as in Step 4.


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14. To the other plate from Step 12, add 10 ␮L of ␧-aminocaproyl-D-alanyl-D-alanine, before adding the S. aureus inoculum and incubating as in Step 3. Record Ii values as in Step 4. 15. Identify as hits those samples retaining Ii values ≥80 in both Steps 13 and 14 (see Note 4). The above procedure actually consists of a primary assay (inhibition of S. aureus growth), followed by three secondary assays (lack of inhibition of L-form growth; persistence of S. aureus inhibition after treating the sample with penicillinases; and persistence of S. aureus inhibition in the presence of an excess of ␧-amino-caproyl-D-alanyl-D-alanine). This screening algorithm selects for cell-wall-acting antibiotics, discarding two of the most frequent inhibitor classes found in microbial fermentation extracts (␤-lactams and glycopeptides), empirically providing a substantial enrichment in cell-wall-acting lantibiotics. However, as any screening algorithm, it is not going to be infallible and a number of false positives may go through the screening. These can be best discarded by chemical means, identifying characteristic properties during further processing of the hits. It would be impossible to provide detailed protocols for the identification and characterization of newly discovered lantibiotics, since procedures would have to be adjusted to the producer strains and to the properties of the compound(s) under investigation. Instead, we provide some useful tips on the recognition of lantibiotics in fermentation broth extracts and in the subsequent structural elucidation of interesting compounds. Since lantibiotics are relatively high molecular weight compounds, they can be identified by their UV absorption and mass spectrometry properties. Usually, an HPLC fractionation (18) allows the identification of fractions containing the bioactive compounds, to which UV and MS data can be assigned. Most lantibiotics have a molecular mass above 2,000 and display a typical peptide UV spectrum. The presence of lanthionine residues and dehydroamino acids can be revealed by selective modification (19). Structural elucidation is best performed by employing a combination of MS and NMR spectroscopy, possibly assisted by selective chemical derivatization and genomic-derived sequence of the lanA gene. As the size of the lantibiotic and the number of thioether rings increase, a combination of techniques should be employed to avoid misinterpretation of the data derived from a single analysis. A recent example demonstrates a substantial revision of a lantibiotic structure reported just 2 years before (13). 3.2. Evaluation of Antibacterial Lantibiotics

The scope of this section is to provide methods for evaluating antibacterial lantibiotics useful for treating bacterial infections in humans. Once a new lantibiotic has been selected for further

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evaluation, its activity against a panel of representative microorganisms should be determined in standard and ad hoc experimental conditions. The initial selection of test microorganisms should be based on literature data documenting the antibacterial spectrum of different lantibiotics. Numerous studies have shown that lantibiotics have low MICs against many clinically relevant Gram-positive bacterial species, belonging to the genera Enterococcus, Listeria, Staphylococcus, Streptococcus, Bacillus, and others (20, 21). Although lantibiotics share a somewhat similar profile, not all compounds possess the same potency and spectrum. For example, Listeria monocytogenes is relatively insensitive to nisin (MICs between 200 and 1,000 mg/L), while highly susceptible to mersacidin and NAI-107 (12). Furthermore, because Grampositive bacteria do produce lantibiotics, some strains may produce a lantibiotic related to the one under study, and thus be naturally resistant to the compound under investigation. Lantibiotics such as mersacidin and actagardine display considerable activity against S. aureus, including methicillinresistant strains (MRSA). While the glycopeptide antibiotic vancomycin can be used to treat MRSA and enterococcal infections, vancomycin-insensitive and vancomycin-resistant strains have emerged. Independent of the mechanism of vancomycin resistance (e.g., redirection of cell-wall biosynthesis as in enterococci or a thickened cell wall as in staphylococci), vancomycinresistant strains remain sensitive to mersacidin (22–24) and to other lantibiotics, such as NAI-107 (unpublished data), indicating that cross-resistance does not represent an immediate problem. Several lantibiotics, including nisin and NAI-107, have excellent activity against antibiotic-resistant streptococci. In particular, both compounds are very active against clinical isolates of Streptococcus pneumoniae, including penicillin-resistant strains (21). Some lantibiotics have shown activity against Mycobacterium tuberculosis (25), an aspect that deserves further evaluation. Since the actual antibacterial spectrum of a newly discovered lantibiotic is unknown, strains representative of the most clinically relevant pathogens should be included in the first panel of microorganisms to be used for susceptibility assays. An example of an initial microbial panel is provided in Table 3.1. MIC determinations are performed by broth microdilution assays in sterile, polystyrene round-bottom 96-well microtiter plates, according to CLSI procedures (26, 27), as detailed below: 1. Use a different 96-well microtiter plate (see Note 6) for each strain. Dispense 10 ␮L of serial 1:2 dilutions of compounds to be tested in each row of the microtiter plate, using the top row for the growth control (no compound added) and the bottom row for a reference antibiotic.


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2. Prepare the inoculum by dispensing an appropriate amount of the frozen stock into the appropriate medium of Table 3.1 (see Note 7) to obtain a final titer of 1–5 × 106 CFU/mL for Mycobacterium smegmatis and 1–5 × 105 CFU/mL for the other strains (see Note 8). 3. Add 90 ␮L of the bacterial inoculum to each well of the microtiter plate from Step 1 and incubate plates at 37◦ C for 72 h (M. smegmatis) or for 20–24 h (all other strains). 4. For each compound and each strain, the MIC is defined as the lowest concentration causing complete suppression of visible bacterial growth. Further characterization of new lantibiotics should include some Gram-negative pathogens and anaerobic Gram-positive bacteria. A list of suggested microorganisms and relative culture conditions is reported in Table 3.2. To improve the outcome of the in vitro profiling of new lantibiotics, we recommend albumin precoating of plastic wells, measuring activity at different pHs (see Note 7) and using cation-adjusted media (see Note 8). The addition of human or rat serum may cause a reduction in the activity of some lantibiotics, presumably due to significant binding to serum protein(s). However, this is not a general phenomenon, and odd behaviors can also be observed; for example, serum proteins reduce the activity of mutacin against S. pneumoniae, but increase its activity against S. aureus. Sera from different sources should be added at a 10–30% concentration. In general, lantibiotics are bactericidal against susceptible organisms, but their bactericidal activity might be limited. It is therefore recommended to evaluate the bactericidal activity of new lantibiotics by time-kill experiments using different strains, such as S. aureus (including MRSA), S. pneumoniae, Enterococcus faecalis, or Enterococcus faecium. The following method for time-kill experiments is recommended by CLSI (28): 1. Pick several colonies of the desired strain from an MHA plate incubated overnight at 37◦ C and disperse them into MHB medium. 2. Incubate cultures under shaking conditions at 37◦ C until an OD600 of 0.2 is reached. 3. Dilute cultures to 1–5 × 106 CFU/mL (approximately 1:10 of the culture obtained in Step 2) in fresh MHB medium, distribute them into flasks containing the compound at different concentrations (see Note 9), and incubate flasks under shaking conditions at 37◦ C (see Note 10). 4. Withdraw duplicate 0.1 mL aliquots at various time intervals for up to 24 h, including also a time 0 control. 5. Prepare serial 1:10 dilutions of each aliquot in MHB medium, mix with 4 mL MHSA medium, and spread onto MHA plates.

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6. Score colonies after 24 h at 35ºC. 7. Calculate the CFU in the original culture from the different dilutions, average out the results from the duplicate aliquots, and plot for each antibiotic concentration the observed CFU/mL as a function of time. Once the in vitro antimicrobial profile and the bactericidal activity of the selected lantibiotic have been defined, it is important to confirm that the compound is equally active on a larger number of strains, including fresh clinical isolates. At least 10 different isolates should be used for each species to be investigated.

4. Conclusions The examples described above provide detailed methods for discovering lantibiotics from actinomycetes and other bacterial strains and for characterizing the antibacterial properties of newly discovered lantibiotics. We have also tried to provide general considerations to guide the reader in understanding the procedures and the context in which they are executed. Additional characterizations will depend on the properties of the lantibiotic under investigation. Furthermore, as our understanding of this poorly explored class expands, additional bioactivities may be discovered and new tools may become available.

5. Notes 1. Positive and negative controls are represented by 10% DMSO and 0.1 ␮g/mL penicillin G, respectively. Any other cell-wall-active antibiotic can be used in place of penicillin G, as long as it does not interfere with growth of L -forms (see also Note 3). 2. The >90% value as a positive threshold is a suggested value based on the authors’ experience. Because assay variability is strongly dependent on the equipment used, it is recommended to run the assay system through a pilot study to establish statistically relevant thresholds for accepting or discarding a sample after each test. Refer to specialized literature on the topic (29). 3. Positive and negative controls are represented by 0.1 ␮g/mL penicillin G and 5 ␮g/mL chloramphenicol, respectively. Any other antibiotic active on L-forms can be used in place of chloramphenicol.


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4. The ≥80% value for reconfirmation of a positive and the ≤40% value for accepting a sample because it does not affect growth of the L-form are again suggestions based on our experience. See also Note 2. 5. With microbial fermentation extracts, the probability that a sample retains a signal above threshold decreases with its dilution, so in many cases the measured DI /DG ratio may only be ≥2. These samples may be retained for further analysis, but they may not confirm their lack of activity against L-forms when more concentrated preparations become available. 6. Since lantibiotics may bind to plastic surfaces, it is recommended to pre-coat the wells with 0.02% BSA. To this end, 100 ␮L are distributed in each well and, after 30 min at room temperature, excess liquid is removed and the microtiter plates are briefly dried in a sterile hood. 7. The stability of different lantibiotics to pH may vary. MICs against selected organisms (preferably S. aureus, S. pneumoniae, L. monocytogenes) should be determined at different pHs, by adjusting the pH of the corresponding medium (see Table 3.1) with 1 N HCl or NaOH, as appropriate. It is recommended to check and, if necessary, adjust the pH also after autoclaving the medium. 8. Because of the charged nature of lantibiotics, the use of cation-adjusted medium is advisable, since the presence of CaCl2 enhances the activity of some lantibiotics (30, 31). 9. Use three or four different concentrations of the lantibiotic under investigation, starting at the MIC value for that strain and increasing the concentration up to 10× MIC. 10. Use one flask as growth control (no antibiotic added) and a second flask as positive control, adding a reference antibiotic at a single concentration.

Acknowledgments We are grateful to Wilfred van der Donk and Mike Dawson for sharing information ahead of publication. References 1. Chatterjee, C., Paul, M., Xie, L., and van der Donk, W. A. (2005) Biosynthesis and mode of action of lantibiotics. Chem. Rev. 105, 633–684.

2. Willey, J. M. and van der Donk, W. A. (2007) Lantibiotics: peptides of diverse structure and function. Annu. Rev. Microbiol. 61, 477–501.

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3. Märki, F., Hänni, E., Fredenhagen, A., and van Oostrum, J. (1991) Mode of action of the lanthionine-containing peptide antibiotics duramycin, duramycin B and C, and cinnamycin as indirect inhibitors of phospholipase A2. Biochem. Pharmacol. 42, 2027–2035. 4. Cloutier, M. M., Guernsey, L., Mattes, P., and Koeppen, B. (1990) Duramycin enhances chloride secretion in airway epithelium. Am. J. Physiol. 259, C450–C454. 5. Molina y Vedia, L. M., Stutts, M. J., Boucher, J. R. C., and Henke, D. C. (1995) U.S. Patent No. 5,716,931. 6. Cox, C. R., Coburn, P. S., and Gilmore, M. S. (2005) Enterococcal cytolysin: a novel two component peptide system that serves as a bacterial defense against eukaryotic and prokaryotic cells. Curr. Protein Pept. Sci. 6, 77–84. 7. Kodani, S., Hudson, M. E., Durrant, M. C., Buttner, M. J., Nodwell, J. R., and Willey, J. M. (2004) The SapB morphogen is a lantibiotic-like peptide derived from the product of the developmental gene ramS in Streptomyces coelicolor. Proc. Natl. Acad. Sci. USA 101, 11448–11453. 8. Kodani, S., Lodato, M. A., Durrant, M. C., Picart, F., and Willey, J. M. (2005) SapT, a lanthionine-containing peptide involved in aerial hyphae formation in the streptomycetes. Mol. Microbiol. 58, 1368–1380. 9. Tillotson, R. D., Wösten, H. A., Richter, M., and Willey, J. M. (1998) A surface active protein involved in aerial hyphae formation in the filamentous fungus Schizophyllum commune restores the capacity of a bald mutant of the filamentous bacterium Streptomyces coelicolor to erect aerial structures. Mol. Microbiol. 30, 595–602. 10. Kellner, R., Jung, G., Josten, M., Kaletta, C., Entian, K. D., and Sahl, H. G. (1989) Pep5: structure elucidation of a large lantibiotic. Angew. Chem. 101, 618–621. 11. Pag, U. and Sahl, H. G. (2002) Multiple activities in lantibiotics – models for the design of novel antibiotics? Curr. Pharm. Des. 8, 815–833. 12. Castiglione, F., Lazzarini, A., Carrano, L., Corti, E., Ciciliato, I., Gastaldo, L., Candiani, P., Losi, D., Marinelli, F., Selva, E., and Parenti, F. (2008) Determining the structure and mode of action of microbisporicin, a potent lantibiotic active against multiresistant pathogens. Chem. Biol. 15, 22–31. 13. Maffioli, S. I., Potenza, D., Vasile, F., De Matteo, M., Sosio, M., Marsiglia, B., Rizzo,

14.

15.

16.

17.

18.

19.

20.

21.

22.

23.

24.

V., Scolastico, C., and Donadio, S. (2009) Structure revision of the lantibiotic 97518. J. Nat. Prod. DOI: 10.1021/np800794y. Li, B., Cooper, L. E., and van der Donk, W. A. (2009) In vitro studies of lantibiotic biosynthesis. Meth. Enzymol. 458, 533–558. Cortés, J., Appleyard, A. N., and Dawson, M. J. (2009) Whole-cell generation of lantibiotic variants. Meth. Enzymol. 458, 559–574. Somma, S., Merati, W., and Parenti, F. (1977) Gardimycin, a new antibiotic inhibiting peptidoglycan synthesis. Antimicrob. Agents Chemother. 11, 396–401. Dodd, H., Gasson, M., Mayer, M., and Narbad, A. (2006) Identifying lantibiotic gene clusters and novel lantibiotic genes. WO 2006/111743. Donadio, S., Monciardini, P., and Sosio, M. (2009) Approaches to discovering novel antibacterial and antifungal agents. Meth. Enzymol. 458, 3–28. Meyer, H. E., Heber, M., Eisermann, B., Korte, H., Metzger, J. W., and Jung, G. (1994) Sequence analysis of lantibiotics: chemical derivatization procedures allow a fast access to complete Edman degradation. Anal. Biochem. 223, 185–190. Brumfitt, W., Salton, M. R., and HamiltonMiller, J. M. (2002) Nisin, alone and combined with peptidoglycan-modulating antibiotics: activity against methicillin-resistant Staphylococcus aureus and vancomycinresistant enterococci. J. Antimicrob. Chemother. 50, 731–734. Goldstein, B. P., Wei, J., Greenberg, K., and Novick, R. (1998) Activity of nisin against Streptococcus pneumoniae, in vitro, and in a mouse infection model. J. Antimicrob. Chemother. 42, 277–278. Brötz, H., Bierbaum, G., Markus, A., Molitor, E., and Sahl, H. G. (1995) Mode of action of the lantibiotic mersacidin: inhibition of peptidoglycan biosynthesis via a novel mechanism? Antimicrob. Agents Chemother. 39, 714–719. Brötz, H., Bierbaum, G., Reynolds, P. E., and Sahl, H. G. (1997) The lantibiotic mersacidin inhibits peptidoglycan biosynthesis at the level of transglycosylation. Eur. J. Biochem. 246, 193–199. Brötz, H., Bierbaum, G., Leopold, K., Reynolds, P. E., and Sahl, H. G. (1998) The lantibiotic mersacidin inhibits peptidoglycan synthesis by targeting lipid II. Antimicrob. Agents Chemother. 42, 154–160.

Strategies for the Isolation and Characterization of Antibacterial Lantibiotics 25. Bavin, E. M., Beach, A. S., Falconer, R., and Friedman, R. (1952) Nisin in experimental tuberculosis. Lancet 259, 127–129. 26. NCCLS document M100-S16. (2006) Performance standards for antimicrobial susceptibility testing. 27. NCCLS document M7-A7. (2008) Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically. 28. NCCLS document M26-A. (2005) Methods for determining bactericidal activity of antimicrobial agents. 29. Zhang, J. H., Chung, T. D., and Oldenburg, K. R. (1999) A simple statistical parameter

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for use in evaluation and validation of high throughput screening assays. J. Biomol. Screen 4, 67–73. 30. Barrett, M. S., Wenzel, R. P., and Jones, R. N. (1992) In vitro activity of mersacidin (M87-1551), an investigational peptide antibiotic tested against Gram-positive bloodstream isolates. Diagn. Microbiol. Infect Dis. 15, 641–644. 31. Schneider, T. R., Kärcher, J., Pohl, E., Lubini, P., and Sheldrick, G. M. (2000) Ab initio structure determination of the lantibiotic mersacidin. Acta Crystallogr. D Biol. Crystallogr. 56, 705–713.

Chapter 4 Expression and Purification of Recombinant ␣-Defensins and ␣-Defensin Precursors in Escherichia coli Sharel Figueredo, Jennifer R. Mastroianni, Kenneth P. Tai, and Andre´ J. Ouellette Abstract Recombinant expression of ␣-defensins can be obtained at efficient levels in Escherichia coli. Amplified ␣-defensin or pro-␣-defensin coding cDNA sequences are cloned directionally between EcoRI and SalI sites of the pET-28a expression vector and expressed in E. coli BL21 RIS cells. Cells growing exponentially in nutrient-rich liquid medium are induced to express the recombinant protein by addition of 50 mM isopropyl ␤-D-1-thiogalactopyranoside for 3–6 h. After bacterial cells collected by centrifugation are lysed in 6 M guanidine-HCl under non-reducing conditions, the expressed defensin fused to its 6xHis-34 amino acid N-terminal fusion partner is purified by affinity chromatography on nickel-NTA columns. A Met codon introduced at the N terminus of expressed Met-free peptides provides a unique CNBr cleavage site, enabling release of the ␣-defensin free of ancillary residues by sequential C18 RP-HPLC. Molecular masses of C18 RP-HPLC purified peptides are confirmed by MALDI-TOF mass spectrometry, and peptide homogeneity is assessed using analytical RP-HPLC and acid-urea polyacrylamide gel electrophoresis. ␣-Defensins prepared in this manner are biochemically equivalent to the natural molecules. Key words: pET-28a, directional cloning, affinity chromatography, reverse-phase high-performance liquid chromatography, matrix-assisted laser desorption ionization time-of-flight mass spectrometry, acid-urea polyacrylamide gel electrophoresis.

1. Introduction Defensins are one of two antimicrobial peptide (AMP) superfamilies, the other being the cathelicidins, with roles in the mammalian innate immune response (1). Members of the ␣-defensin subfamily occur at two primary sites: as abundant constituents of neutrophil azurophil granules (2, 3) the dense core secretory A. Giuliani, A.C. Rinaldi (eds.), Antimicrobial Peptides, Methods in Molecular Biology 618, DOI 10.1007/978-1-60761-594-1 4, © Springer Science+Business Media, LLC 2010

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granules of Paneth cells in small intestinal crypts from which they are secreted into the small intestinal lumen (4, 5). Typically, these ∼ 4 kDa bactericidal peptides are cationic, amphipathic, and constrained by a highly conserved tridisulfide array with CysI -CysVI , CysII -CysIV , and CysIII -CysV disulfide pairings (1, 6). Their mode of action involves disruption of bacterial cell membranes mediated in part by selective interactions with electronegative target cell envelopes (7–9). Myeloid and Paneth cell ␣-defensins derive from ∼10 kDa pre-propeptides that contain canonical signal sequences, acidic proregions, and a ∼4 kDa mature ␣-defensin peptide in the C-terminal portion of the precursor (10–13). Despite having highly diverse primary structures (14, 15), ␣-defensins uniquely retain conserved biochemical features that include the invariant disulfide array (16), a canonical Arg-Glu salt bridge, a conserved Gly residue at position CysIII+8 , and high Arg content relative to Lys (17, 18). Although functional determinants of ␣-defensin microbicidal activity have been suggested by inspection of sequences or interpreted from comparisons of bactericidal peptide assays reported independently by numerous laboratories, few ␣-defensins have been subjected to a systematic structure–activity analysis in which residue positions critical for peptide function have been tested by induction of loss of function following site-directed mutagenesis. This latter approach has been pursued by production of peptide variants by solid-phase synthesis (18–21) or by using recombinant approaches (7, 20, 22–24). Here, we will consider the production of ␣-defensins by recombinant approaches in Escherichia coli, because the method is inexpensive and flexible and readily can be adapted to the expression of precursor forms which exceed the chain length for optimal synthesis in solid phase.

2. Materials 2.1. Expression Cloning of α -Defensin Coding Sequences

1. pET-28a plasmid DNA (EMD/Novagen, EMD Chemicals, Gibbstown, NJ, USA). 2. GeneAmp PCR Core Reagents (Applied Biosystems, Foster City, CA, USA). 3. QIAEX II Gel Extraction Kit (Qiagen, Inc., USA, Valencia, CA, USA). 4. TOPO TA Cloning Kit, with pCR2.1-TOPO vector (Invitrogen, Carlsbad, CA, USA). 5. DNA Ligation Kit Ver. 2, Buffer I (Takara Bio obtained via Fisher Scientific, Pittsburgh, PA, USA).

Recombinant Production of ␣-Defensins

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6. Kanamycin (Fisher Scientific) stock solution: dissolve 100 mg/mL in deionized water, filter sterilize, and store at –20◦ C. 7. Trypticase Soy Agar plates: combine 12 g BactoTM agar, 18 g BactoTM Tryptic Soy Broth with 600 mL H2 O. Stir the mixture for 30 min, sterilize by autoclaving, stir aseptically, cool to ∼ 50◦ C, add kanamycin from stock solution to a final concentration of 50 ␮g/mL. 8. Qiaprep Spin Miniprep Kit (Qiagen). 9. E. coli XL-2 Blue Ultracompetent cells (Stratagene, La Jolla, CA, USA). 10. E. coli BL21(DE3)pLysS competent cells (Stratagene). 2.2. Expression of Recombinant α -Defensins

R 1. Six 2,800 mL, wide-mouth PYREX Fernbach-style culture flasks with triple baffles located at the center of the flask bottom to achieve maximal oxygen transfer to culture medium.

2. Stock solutions for Terrific Broth (TB) culture medium: (A) 12 g Bacto tryptone (BD Biosciences, San José, CA, USA), 24 g Bacto yeast extract (BD), 4 mL glycerol, 900 mL deionized water. Dissolve all solids and autoclave for 45 min. (B) Potassium phosphate buffer: dissolve 23.1 g potassium phosphate (KH2 PO4 , Fisher Scientific) and 125.4 g potassium phosphate dibasic (K2 HPO4 anhydrous, Fisher Scientific) in deionized water to a final volume of 1 L and autoclave for 15 min. (C) 30% Dextrose: dissolve 30 g anhydrous dextrose (Fisher Scientific) in deionized water to a final volume of 100 mL and autoclave for 15 min. (D) Kanamycin (Fisher Scientific) stock solution (see Section 2.1, Step 4). 3. Beckman model GS-6R benchtop centrifuge. 4. Incubator shaker, Model C25KC (New Brunswick Scientific, Edison, NJ, USA), or comparable instrument with capacity for six 2,800 mL Fernbach-style flasks. 5. Isopropyl-␤-D-1-thiogalactopyranoside (IPTG, Fisher Scientific) solution: dissolve 25 g IPTG in 105 mL deionized water. Store as 1.2 mL aliquots at 4◦ C. 6. Nalgene 1,000 mL wide-mouth polycarbonate (PP GF20 resin) centrifuge bottles with sealing cap for FIBERLite F84X1000y rotor (FIBERLite Centrifuge, Santa Clara, CA, USA). 7. Sorvall RC-26 Plus superspeed centrifuge. 8. Lysis buffer: to prepare 6 M guanidine-HCl and 100 mM Tris-HCl, dissolve 573.2 g guanidine hydrochloride (Calbiochem, EMD Chemicals, Gibbstown, NJ, USA) and

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12.1 g Tris (Bio-Rad, Hercules, CA, USA) in deionized water, adjust to pH 8.1, and add water to 1 L. 9. Branson Sonifier 450 (Branson Ultrasonics Corp, Danbury, CT, USA), constant cycle, output control set at 5. 10. FIBERLite rotor F21-8X50, rotor code SA-600. 2.3. Cleavage of Fusion Proteins with CNBr

1. Nickel-nitrilotriacetic acid (Ni-NTA Superflow, Qiagen). 2. Column elution buffer: 6 M guanidine-HCl (Calbiochem), 20 mM Tris-HCl (pH 8.1). 3. A standard 100 mL chromatography column, in our case a 2.5 × 23 cm Kontes column (Kimble-Chase, Vineland, NJ, USA). 4. 1 M imidazole, 6 M guanidine-HCl, 20 mM TrisHCl (pH 6.4): prepare by dissolving 69.08 g imidazole (Sigma), 573.2 g guanidine hydrochloride (Calbiochem, EMD Chemicals, Gibbstown, NJ, USA), and 2.42 g Tris (Bio-Rad, Hercules, CA, USA) in deionized water, adjust to pH 8.1, and add water to 1 L final volume. 5. Spectra/Por 3 membranes (Spectrum Laboratories, Inc., Rancho Dominguez, CA) immersed in deionized water for at least 1 h before use. 6. N2 gas cylinders (Airgas West, Santa Ana, CA, USA). 7. Cyanogen bromide (CNBr) (Fisher Scientific) solution: dissolve fresh at 20 mg/mL in 80% formic acid (Sigma-Aldrich, St. Louis, MO, USA). All procedures should be performed in chemical fume hood. 8. 5% acetic acid: dissolve 50 mL glacial acetic acid (Fisher Scientific, ACS certified) in 950 mL dH2 O.

2.4. Analytical Acid-Urea Polyacrylamide Gel Electrophoresis (AU-PAGE)

1. Acrylamide solutions. Solution A (60% acrylamide and 1.6% bisacrylamide): dissolve 1,200 g acrylamide (Fisher Scientific) and 32.0 g bisacrylamide (Fisher Scientific) with H2 O in a 2 L beaker to a volume of ∼ 1,800 mL. Place beaker in 50◦ C water bath, dissolve solids with vigorous stirring, adjust volume to 2 L, filter solution through Whatman #4 paper, aliquot, and store at ambient temperature in foil-wrapped bottles. Solution B (43.2% acetic acid, 4% N,N,N ,N -tetramethylethylenediamine, TEMED): for 1 L combine 432 mL glacial acetic acid, 40 mL TEMED (Fisher Scientific), and 528 mL water. 2. Ammonium persulfate solution: 0.50 g in 5 mL water, made fresh. 3. AU-PAGE electrode buffer: 5% acetic acid in deionized water.


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4. Sample loading buffer (3X): dissolve 54 g urea (ultra pure, MP Biomedicals, LLC, Solon, OH, USA) in H2 O to a volume of 95 mL. When dissolved, add ∼1 teaspoon AG 501-X8, 20–50 mesh mixed bed resin (Bio-Rad), stir 5 min, filter decant supernatant, add 5 mL glacial acetic acid and methyl green (Sigma-Aldrich) until the solution is a dark blue-green color. Store in 1 mL aliquots at –20◦ C. 5. 0.9% agarose: 1.35 g agarose (Cambrex Bio Science Rockland, Rockland, ME, USA) up to 150 mL with H2 O. 2.5. Reversed-Phase High-Pressure Liquid Chromatography (RP-HPLC)

1. Preparative RP-HPLC: Waters PrepLC 25 mm Module column model 25 M configured with a Waters Delta Prep 4000 Preparative PrepLC System Controller and a Waters 486 Tunable Absorbance Detector (Waters Corporation, Milford, MA; USA). 2. Semi-Preparative and analytical RP-HPLC: Vydac SemiPrep C18 column 218TP510 and Vydac Analytical C18 column 218TP54 (Grace, Deerfield, IL, USA) configured with Waters Automated Gradient Controllers, Waters Model 510 pumps, and Waters 484 Tunable Absorbance Detectors. 3. Water (HPLC) from Fisher Scientific and acetonitrile (Fisher Scientific, Optima grade), both containing 0.1% trifluoroacetic acid (TFA, HPLC/Spectro grade; Pierce, Thermo Fischer Scientific, Rockford, IL, USA) as the ion-pairing agent. 4. Coomassie stain solution (54% H2 O, 30% methanol, 15% formalin, 1% Brilliant Blue): add 1.0 g Brilliant Blue R-250 (Fisher Scientific, electrophoresis grade) to 300 mL methanol (Fisher Scientific) and 550 mL H2 O. When dissolved, add 150 mL formalin (Fisher Scientific, 10% solution). Stir until mixed completely and store in a glass bottle at room temperature. 5. AU-Gel destain solution (74% H2 O, 25% methanol, 1% formaldehyde): to prepare 3 L, combine 1,850 mL H2 O, 650 mL methanol, and 25 mL formaldehyde (Fisher Scientific, ACS certified, 37% w/w). Store in a glass bottle at room temperature. 6. AU-Gel Soak Solution (42% H2 O, 40% methanol, 10% acetic acid, 5% formalin, 3% glycerol): for 2 L, combine 840 mL H2 O, 800 mL methanol, 200 mL glacial acetic acid, 100 mL formalin, and 60 mL glycerol (Fisher Scientific). Store in a glass bottle at room temperature. 7. Bio-Rad GelAir dryer.

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2.6. Matrix-Assisted Laser Desorption Ionization Time-of-flight (MALDI-TOF) Mass Spectrometry

1. ␣-Cyano Matrix: 10 mg/mL ␣-cyano-4-hydroxycinnamic acid (Sigma-Aldrich) dissolved in 60% acetonitrile with 0.1% TFA and stored in 0.5 mL aliquots at –20◦ C. 2. Voyager-DE MALDI-TOF mass Biosystems, Foster City, CA, USA).

spectrometer

(P-E-

3. Methods 3.1. Expression Cloning of α -Defensin Coding Sequences

1. Prepare recombinant mouse ␣-defensins and pro-␣defensins using the pET-28a expression system to produce N-terminal 6xHis-tagged fusion proteins (see Section 2.1, Step 1). For ␣-defensins that lack Met, a unique Met-coding trideoxynucleotide is incorporated 5 - of the first codon of the desired peptide by PCR amplification and cloned inframe with the amino terminal 6XHis in the EcoRI/SalI sites of pET-28a (25, 26). 2. Perform amplification reactions using the GeneAmp PCR Core Reagents (see Section 2.1, Step 2) by incubating reaction mixtures at 95◦ C for 5 min, followed by successive cycles at 60◦ C for 1 min, 72◦ C for 1 min, and 94◦ C for 1 min for 40 cycles. For example, for cloning proCrp4, forward primer pC4-F [5 -GCGCG AATTC ATGGA TCCTA TCCAA AACAC A] was paired with reverse primer pC4R [5 -ATATA TTGT TCAGC GGCGG GGGCA GCAGT ACAA], corresponding to nucleotides 104 to 119 and 301 to 327 in pre-proCrp4 cDNA (27). The underlined codon in the pC4-F primer denotes the Met codon (ATG) that introduces the unique CNBr cleavage site immediately downstream of the GAATTC EcoRI site. Underlined residues in the pC4-R cloning primer denote the SalI recognition site. 3. Following PCR amplification, electrophorese samples (25 ␮L) of individual reactions in 2% agarose gels, stain amplification products with ethidium bromide, excise them, and extract them using QIAEX II according to the manufacturer’s protocol. 4. Clone amplification products in pCR2.1-TOPO (Section 2.1, Step 4). Screen plasmid minipreps for inserts by digestion with EcoRI and subject positive clones to DNA sequence analysis to confirm that the expression sequence is in-frame. 5. Prepare the expression vector by sequential incubation of pET-28a plasmid DNA with SalI overnight followed by 4 h incubation with EcoRI and deproteinize it. Determine vector


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background by transforming competent E. coli XL-2 Blue cells with mock-ligation reactions containing 20 ng samples of EcoRI and SalI-digested pET-28a but without amplified DNA and plating on TSB plates containing 50 ␮g/mL kanamycin (see Note 1). 6. Digest plasmids containing defensin-coding inserts in pCR2.1-TOPO clones with EcoRI and SalI, and gel-purify EcoRI/SalI-digested fragments. 7. Ligate fragments into the EcoRI/SalI-digested pET-28a plasmid DNA and transform into E. coli XL-2 Blue cells for archiving and into E. coli BL21(DE3)pLysS cells for expression. 3.2. Expression of Recombinant α -Defensin Fusion Proteins

1. For large-scale preparation of recombinant ␣-defensins, streak BL21(DE3)pLysS cells transformed with pET-28a ␣-defensin constructs onto TB plates containing 70 ␮g/mL kanamycin to obtain isolated colonies. Inoculate 100 mL of kanamycin-TB broth with a single colony and grow overnight at 37◦ C in a model C25KC incubator shaker. 2. After overnight growth, transfer the culture to two 50 mL Falcon tubes, centrifuge at 3,000 rpm for 10 min in a Beckman GS-6R centrifuge, and resuspend the bacterial cell pellet in 6 mL TB as concentrated inoculum. 3. To each autoclaved 2,800 mL Fernbach-style flask, add 900 mL of sterile Bacto Tryptone, yeast extract, glycerol solution, 100 mL of potassium phosphate buffer, 5 mL 30% dextrose solution, and 10 mg/mL kanamycin from stock solution to a final concentration of 70 ␮g/mL kanamycin (see Section 2.2, Step 2). Prewarm medium to 37◦ C, inoculate each flask with 1 mL of the concentrated inoculum, and grow cells at 37◦ C in the model C25KC incubator shaker at a setting of 250 rpm. Monitor the optical density of the culture at 600 nm until the exponentially growing cells reach an A600 value of 0.70–0.80, at which point production of recombinant proteins is induced by addition of 100 ␮M IPTG under kanamycin selection (see Note 2). 4. After 6 h at 37◦ C, transfer cultures to 1,000 mL wide-mouth polycarbonate (PP GF20 resin) centrifuge bottles with sealing caps and centrifuge for 5 min at 5,000 rpm in a FIBERLite F8-4X1000y rotor in a Sorvall RC-26 Plus superspeed centrifuge. Decant supernatants from deposited bacterial cells, decontaminate with bleach, and store deposited bacterial cell pellets at –20◦ C overnight (see Note 3). 5. Lyse cells by resuspending the bacterial cell pellets in lysis buffer (see Section 2.2, Step 8), followed by sonication at

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70% power and 50% duty cycle for 2 min using a Branson Sonifier 450. Clarify lysates by centrifugation at 30,000×g for 30 min at 4◦ C in a FIBERLite F21-8X50 rotor using rotor code SA-600 in a Sorvall RC-26 Plus superspeed centrifuge. Fusion proteins are purified immediately after lysate clarification (see Section 3.3, below). 3.3. Affinity Purification and Cleavage of Fusion Protein

1. Recombinant His-tagged ␣-defensin fusion peptides are purified by nickel-nitrilotriacetic acid (Ni-NTA) resin affinity chromatography (22). Subsequently, ␣-defensins are cleaved from fusion proteins with CNBr cleavage, and ␣defensins are recovered and purified by RP-HPLC. Incubate cell lysates with Ni-NTA resin at a ratio of 25:1 (v/v) in 6 M guanidine-HCl, 20 mM Tris-HCl (pH 8.1) (see Section 2.3, Step 2) for 4 h at 4◦ C. Pour the mixture into a 2.5 × 23 cm Kontes column fitted with a polyethylene drain tube and a small thumb-clamp closure to maintain a flow rate of ∼ 1 mL/min. 2. Wash the resin lysate mixture with 10–20 column bed volumes of 6 M guanidine-HCl, 20 mM Tris-HCl (pH 8.1) to remove proteins and peptides non-specifically associated with the resin. Fusion proteins, containing a 6xHis tag near the fusion protein N terminus, a 26 amino acid spacer, and the ␣-defensin (Fig. 4.1) are then eluted from the resin with 2 bed volumes of 1 M imidazole in 6 M guanidine-HCl, 20 mM Tris-HCl (pH 6.4; see Section 2.3, Step 4), dialyzed in Spectra/Por 3 membranes against 3 × 10 L changes of 5% acetic acid and lyophilized. CNBr cleavage site

Linker sequence for pET-28a: 34 amino acids upstream of the EcoRIsite: MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGS(EF)MET- peptide TGATGASalI 6x-His EcoRI Stops

Fig. 4.1. General features of pET-28a/␣-defensin fusion proteins. The endogenous initiating methionine codon of the pET-28a codes for a 34 amino acid fusion protein immediately N-terminal of the expressed defensin peptide. Residue positions 5–10 form the 6xHis affinity tag, and the arrow indicates the position of the introduced Met residue that provides the unique CNBr cleavage site. Methionine residues in the pET-28a fusion protein are shown in bold.

3. The Met residue added immediately before the N terminus of each ␣-defensin or pro-␣-defensin peptide, as exists in human pro-␣-defensin-1 (13), provides a cyanogen bromide (CNBr) cleavage site for separating the recombinant ␣-defensin molecule from the remainder of the His-tagged fusion peptide (Fig. 4.1). To this end, dissolve lyophilized fusion proteins in 80% formic acid, transfer to foil-wrapped polypropylene tubes to which solid CNBr is added to a final concentration of 10 mg/mL CNBr, purge with N2 , then


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seal tubes. Incubate samples under N2 overnight at 25◦ C in a chemical fume hood. Cleavage reactions are terminated by addition of 10 vol. H2 O followed by freezing and lyophilization. Then dissolve the CNBr-cleaved peptide samples in 5% acetic acid and store at 4◦ C prior to purification by RPHPLC (see Section 3.5). 3.4. Preparation of AU-PAGE gels

1. AU-PAGE is a superior system for separation of small cationic peptides on the basis of their electropositive chargeto-size ratios (28). Running gels are poured in a standard vertical slab gel system. Because longer gels give better resolution, a custom system using 18 × 25 cm plates and 18 × 1 cm spacers of 1.5 mm thickness is used routinely. Plates are clamped with binder clips and sealed with molten agarose (see Section 2.4, Step 5). 2. To prepare five 20% polyacrylamide running gels, combine 48 g urea, 47.45 mL H2 O, 53.45 mL solution A (Section 2.4, Step 1), 20 mL solution B (Section 2.4, Step 1), and 3 mL 10% ammonium persulfate solution (Section 2.4, Step 2). Dissolve completely and pour into the plate assembly, leaving approximately 3 cm above the gel solution free for addition of the stacking gel. The freshly poured gel is overlain with water and polymerizes in ∼ 60 min. 3. To prepare 7.5% polyacrylamide stacking gel solution for five gels, combine 12 g urea, 20.25 mL H2 O, 5 mL solution A (Section 2.4, Step 1), 5 mL solution B (Section 2.4, Step 1), 0.75 mL AP solution (Section 2.4, Step 2), and dissolve all solids. 4. Remove water layer from the running gel, pour stacker, insert combs, overlay with water. The stacking gel polymerizes in ∼ 60 min after which combs are removed, and gels are “pre-run” overnight using 5% acetic acid electrode buffer at 150 V. Because proteins migrate through AU gels as fully protonated forms, the polarity is reversed compared to SDSPAGE, that is, the anode is the negative electrode (see Note 4). After the pre-run, the electrode buffer is discarded. Gels may be used immediately or assembled gels may be wrapped in Saran Wrap and stored at 4◦ C for several days.

3.5. Peptide Purification Using RP-HPLC

1. ␣-Defensins are purified to homogeneity using a reiterative C18 RP-HPLC approach (29). After CNBr cleavage, Crp4 peptides are separated from the 36 amino acid 6xHistag fusion partner by chromatography on a Waters PrepLC 25 mm Module column model 25 M. After sample injection, proteins and peptides are eluted using a 10–60% linear acetonitrile gradient developed for 25 min at a flow rate of 20 mL/min. Samples of individual fractions are lyophilized

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and analyzed in 20% AU-PAGE gels (see Section 3.4) and stained to identify column fractions that contain putative ␣-defensins based on co-migration with ␣-defensin or pro-␣defensin peptide standards. Protein samples are lyophilized prior to electrophoresis and dissolved in ≤ 15 ␮L 1X sample buffer and electrophoresed with fresh 5% acetic acid running buffer at 100 V for sample loading, then increase to 200 V for 3–6 h. After electrophoresis, gels are fixed, stained with Coomassie stain solution and destained (see Section 2.5, Step 4 and 5) submerged in AU-Gel Soak Solution (see Section 2.5, Step 6) for 1 h, and dried using a BioRad GelAir dryer (see Section 2.5, Step 7 and Note 5). The putative defensin-containing column fractions from preparative RP-HPLC (Fig. 4.2a, boxed region) are then concentrated in a high-capacity Speed-Vac to evaporate the acetonitrile, pooled, lyophilized, dissolved in 5% acetic acid, and subjected to further RP-HPLC purification.

Fig. 4.2. AU-PAGE analysis of recombinant Crp4 purification. Samples of individual fractions from preparative (a), semipreparative (b), and analytical C18 RP-HPLC (c) were lyophilized for analysis in 20% AU-PAGE gels. After lyophilization, protein samples were dissolved in ≤ 15 ␮L 1X sample buffer, electrophoresed, fixed, and stained with Coomassie stain solution. Boxed regions denote the position of the recombinant Crp4 peptide at each purification stage. Recombinant control Crp4 standard peptides are shown in the left lane of each gel.

2. Recombinant peptides are purified to homogeneity by sequential semi-preparative and analytical RP-HPLC. After injection of the pooled putative ␣-defensin sample from preparative RP-HPLC, the Vydac 218TP510 (C18) column is developed using a 20–40% linear acetonitrile gradient developed for 60 min at a flow rate of 2 mL/min. As before, aliquot samples of individual column fractions are lyophilized and assayed for putative ␣-defensins by comigration with appropriate ␣-defensin peptide standards in AU-PAGE analyses (Fig. 4.2b, boxed region). MALDITOF MS determinations (see Section 3.6 below) are made to confirm whether column fractions with apparent recombinant proteins by AU-PAGE contain peptides with appropriate molecular masses. Column fractions containing recombinant peptide (Fig. 4.2b, boxed region) are combined and


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concentrated by Speed-Vac evaporation of acetonitrile and subsequent lyophilization as before. Samples are subjected to the final purification separation on analytical RP-HPLC. A Vydac analytical 218TP54 column is developed with a linear 15–25% acetonitrile gradient for 60 min at a 1 mL/min flow rate. Again, aliquot samples of individual column fractions are lyophilized and the homogeneity of the purified recombinant ␣-defensin is assessed by co-migration with appropriate ␣-defensin peptide standards in AU-PAGE analyses (Fig. 4.2c, boxed region). The concentrations of purified recombinant ␣-defensin and pro-␣-defensin solutions are quantified by amino acid analysis services provided, in our case, by the UCLA (http://proteomics.ctrl.ucla.edu/) or UC Davis (http://proteomics.ucdavis.edu/) Proteomics Core Facilities, or spectrophotometrically at 280 nm using extinction coefficients obtained at ExPASy Proteomics Server (http://ca.expasy.org/). For example, ε = 3355 M–1 cm–1 for mouse Crp4. 3.6. Laser Desorption Ionization Time-of-flight (MALDI-TOF) Mass Spectrometry

1. As noted above, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is used extensively to identify and monitor the purification of recombinant ␣-defensins. For this purpose, apply dilute peptide samples (1 ␮L) to stainless steel MALDI sample plates with numbered circles. After application, 1 ␮L aliquots of ␣-cyano matrix is applied to each sample, mixed, and allowed to dry. 2. At this time, perform measurements on a Voyager-DE MALDI-TOF (in our case, available in the Mass Spectroscopy Facility at the Department of Chemistry, University of California Irvine, CA, USA). In the example shown (Fig. 4.2c, boxed region), homogeneously pure recombinant mouse Crp4 had an experimental mass of 3756.3 a.m.u. by MALDI-TOF MS, consistent with the theoretical Crp4 mass of 3755.55 a.m.u. The methods described have proven to be generally successful for the recombinant production of ␣-defensins and pro-␣defensins from mouse and human Paneth cells as well as those from rhesus macaque neutrophils and Paneth cells (24, 30–35) (See Note 6).

4. Notes 1. If more than 50 colonies/10 ng of vector DNA are recovered, EcoRI and SalI digestion of vector DNA sample should be repeated until the background is suitably low.

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2. Although the standard temperature for induction of recombinant protein expression is 37◦ C, recovery of certain defensin peptides may be low when inductions are performed at this temperature. In certain instances, slowing the rate of overall protein production by reducing the temperature during the period of induction frequently improves recovery of fusion protein and properly folded defensins. The optimal induction temperatures are determined empirically by incubating test cultures at temperatures ranging from 30 to 4◦ C for 18 h following addition of IPTG. In this respect, an incubator shaker with refrigeration capability (see Section 2.2, Step 4) may be critical to success in expressing certain defensin peptides or their variants. 3. This freezing step greatly improves subsequent cell lysis as compared to cells that are not frozen. 4. Failure to pre-run gels for a sufficient time under these conditions results with all proteins stacking about half-way down the gel. 5. Stain or destain solutions that lack formaldehyde result in defensin loss from the gel. Also, low sample volume (10–20 ␮L) in 1X sample buffer is critical to good AUPAGE resolution. Up to 1 mg of ␣-defensin or total cellular protein can easily be dissolved in 20 ␮L under these conditions. Lyophilization is a strongly recommended method for concentration of protein samples, because vacuum centrifugation to dryness, i.e., Speed-Vac, may lead to formation of insoluble gels. 6. The use of CNBr to separate the expressed ␣-defensin limits the method described to molecules that are methioninefree, a problem that may be circumvented by replacement of the Met codon with codons that code for enzymatic cleavage sites. For methionine-containing ␣-defensins and pro-␣-defensins, the Met residue introduced by the forward cloning primer (Fig. 4.1) may be replaced with enzymatic cleavage sites such as Asp-Asp-Asp-Asp-Lys, recognized by enterokinase such as the EnterokinaseMax system (Invitrogen). References 1. Selsted, M. E., and Ouellette, A. J. (2005) Mammalian defensins in the antimicrobial immune response. Nat. Immunol. 6, 551–557. 2. Faurschou, M., Sorensen, O. E., Johnsen, A. H., Askaa, J., and Borregaard, N. (2002) Defensin-rich granules of human neutrophils: characterization of secretory

properties. Biochim. Biophys. Acta 1591, 29–35. 3. Borregaard, N., Sorensen, O. E., and Theilgaard-Monch, K. (2007) Neutrophil granules: a library of innate immunity proteins. Trends Immunol. 28, 340–345. 4. Selsted, M. E., and Ouellette, A. J. (1995) Defensins in granules of phagocytic and


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non-phagocytic cells. Trends Cell. Biol. 5, 114–119. Selsted, M. E., Miller, S. I., Henschen, A. H., and Ouellette, A. J. (1992) Enteric defensins: antibiotic peptide components of intestinal host defense. J. Cell. Biol. 118, 929–936. Ouellette, A. J. (2005) Paneth cell alphadefensins: peptide mediators of innate immunity in the small intestine. Springer Semin. Immunopathol. 27, 133–146. Hadjicharalambous, C., Sheynis, T., Jelinek, R., Shanahan, M. T., Ouellette, A. J., and Gizeli, E. (2008) Mechanisms of alphadefensin bactericidal action: comparative membrane disruption by Cryptdin-4 and its disulfide-null analogue. Biochemistry 47, 12626–12634. White, S. H., Wimley, W. C., and Selsted, M. E. (1995) Structure, function, and membrane integration of defensins. Curr. Opin. Struct. Biol. 5, 521–527. Wimley, W. C., Selsted, M. E., and White, S. H. (1994) Interactions between human defensins and lipid bilayers: evidence for formation of multimeric pores. Protein Sci. 3, 1362–1373. Wilson, C. L., Ouellette, A. J., Satchell, D. P., Ayabe, T., Lopez-Boado, Y. S., Stratman, J. L., Hultgren, S. J., Matrisian, L. M., and Parks, W. C. (1999) Regulation of intestinal alpha-defensin activation by the metalloproteinase matrilysin in innate host defense. Science 286, 113–117. Ayabe, T., Satchell, D. P., Pesendorfer, P., Tanabe, H., Wilson, C. L., Hagen, S. J., and Ouellette, A. J. (2002) Activation of Paneth cell alpha-defensins in mouse small intestine. J. Biol. Chem. 277, 5219–5228. Ghosh, D., Porter, E., Shen, B., Lee, S. K., Wilk, D., Drazba, J., Yadav, S. P., Crabb, J. W., Ganz, T., and Bevins, C. L. (2002) Paneth cell trypsin is the processing enzyme for human defensin-5. Nat. Immunol. 3, 583–590. Valore, E. V., and Ganz, T. (1992) Posttranslational processing of defensins in immature human myeloid cells. Blood 79, 1538–1544. Ouellette, A. J. (2006) Paneth cell alphadefensin synthesis and function. Curr. Top. Microbiol. Immunol. 306, 1–25. Ouellette, A. J., and Bevins, C. L. (2001) Paneth cell defensins and innate immunity of the small bowel. Inflamm. Bowel Dis. 7, 43–50. Selsted, M. E., and Harwig, S. S. (1989) Determination of the disulfide array in the human defensin HNP-2. A covalently cyclized peptide. J. Biol. Chem. 264, 4003–4007.

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17. Lehrer, R. I. (2007) Multispecific myeloid defensins. Curr. Opin. Hematol. 14, 16–21. 18. Zou, G., de Leeuw, E., Li, C., Pazgier, M., Zeng, P., Lu, W. Y., Lubkowski, J., and Lu, W. (2007) Toward understanding the cationicity of defensins. Arg and Lys versus their noncoded analogs. J. Biol. Chem. 282, 19653–19665. 19. de Leeuw, E., Burks, S. R., Li, X., Kao, J. P., and Lu, W. (2007) Structure-dependent functional properties of human defensin 5. FEBS Lett. 581, 515–520. 20. Pazgier, M., Li, X., Lu, W., and Lubkowski, J. (2007) Human defensins: synthesis and structural properties. Curr. Pharm. Des. 13, 3096–3118. 21. Wu, Z., Li, X., Ericksen, B., de Leeuw, E., Zou, G., Zeng, P., Xie, C., Li, C., Lubkowski, J., Lu, W. Y., and Lu, W. (2007) Impact of pro segments on the folding and function of human neutrophil alphadefensins. J. Mol. Biol. 368, 537–549. 22. Shirafuji, Y., Tanabe, H., Satchell, D. P., Henschen-Edman, A., Wilson, C. L., and Ouellette, A. J. (2003) Structural determinants of procryptdin recognition and cleavage by matrix metalloproteinase-7. J. Biol. Chem. 278, 7910–7919. 23. Maemoto, A., Qu, X., Rosengren, K. J., Tanabe, H., Henschen-Edman, A., Craik, D. J., and Ouellette, A. J. (2004) Functional analysis of the ␣-defensin disulfide array in mouse cryptdin-4. J. Biol. Chem. 279, 44188–44196. 24. Figueredo, S. M., Weeks, C. S., Young, S. K., and Ouellette, A. J. (2009) Anionic amino acids near the pro-alpha-defensin N terminus mediate inhibition of bactericidal activity in mouse pro-cryptdin-4. J. Biol. Chem. 284, 6826–6831. 25. Satchell, D. P., Sheynis, T., Shirafuji, Y., Kolusheva, S., Ouellette, A. J., and Jelinek, R. (2003) Interactions of mouse Paneth cell alpha-defensins and alpha-defensin precursors with membranes: prosegment inhibition of peptide association with biomimetic membranes. J. Biol. Chem. 278, 13838–13846. 26. Satchell, D. P., Sheynis, T., Kolusheva, S., Cummings, J., Vanderlick, T. K., Jelinek, R., Selsted, M. E., and Ouellette, A. J. (2003) Quantitative interactions between cryptdin-4 amino terminal variants and membranes. Peptides 24, 1795–1805. 27. Ouellette, A. J., Darmoul, D., Tran, D., Huttner, K. M., Yuan, J., and Selsted, M. E. (1999) Peptide localization and gene structure of cryptdin 4, a differentially expressed mouse Paneth cell alpha-defensin. Infect. Immun. 67, 6643–6651.

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28. Selsted, M. E. (1993) Investigational approaches for studying the structures and biological functions of myeloid antimicrobial peptides. Genet. Eng. (NY ) 15, 131–147. 29. Selsted, M. E. (1997) HPLC methods for purification of antimicrobial peptides. Methods Mol. Biol. 78, 17–33. 30. Tanabe, H., Yuan, J., Zaragoza, M. M., Dandekar, S., Henschen-Edman, A., Selsted, M. E., and Ouellette, A. J. (2004) Paneth cell alpha-defensins from rhesus macaque small intestine. Infect. Immun. 72, 1470–1478. 31. Tanabe, H., Qu, X., Weeks, C. S., Cummings, J. E., Kolusheva, S., Walsh, K. B., Jelinek, R., Vanderlick, T. K., Selsted, M. E., and Ouellette, A. J. (2004) Structure-activity determinants in Paneth cell alpha-defensins: loss-of-function in mouse cryptdin-4 by charge-reversal at arginine residue positions. J. Biol. Chem. 279, 11976–11983. 32. Tanabe, H., Ouellette, A. J., Cocco, M. J., and Robinson, W. E., Jr. (2004) Differential effects on human immunodeficiency virus type 1 replication by ␣-defensins with com-

parable bactericidal activities. J. Virol. 78, 11622–11631. 33. Weeks, C. S., Tanabe, H., Cummings, J. E., Crampton, S. P., Sheynis, T., Jelinek, R., Vanderlick, T. K., Cocco, M. J., and Ouellette, A. J. (2006) Matrix metalloproteinase7 activation of mouse Paneth cell pro-alphadefensins: SER43↓ILE44 proteolysis enables membrane-disruptive activity. J. Biol. Chem. 281, 28932–28942. 34. Rosengren, K. J., Daly, N. L., Fornander, L. M., Jonsson, L. M., Shirafuji, Y., Qu, X., Vogel, H. J., Ouellette, A. J., and Craik, D. J. (2006) Structural and functional characterization of the conserved salt bridge in mammalian Paneth cell alpha-defensins: solution structures of mouse Cryptdin-4 and (E15D)Cryptdin-4. J. Biol. Chem. 281, 28068– 28078. 35. Kamdar, K., Maemoto, A., Qu, X., Young, S. K., and Ouellette, A. J. (2008) In vitro activation of the rhesus macaque myeloid alphadefensin precursor proRMAD-4 by neutrophil serine proteinases. J. Biol. Chem. 283, 32361–32368.

Chapter 5 Production of Recombinant Antimicrobial Peptides in Bacteria Mateja Zorko and Roman Jerala Abstract Large quantities of antimicrobial peptides are required for investigations and clinical trials, therefore suitable production method alternative to traditional chemical synthesis is necessary. Production of recombinant antimicrobial peptides in prokaryotic systems has successfully demonstrated the viability of this approach. Production of antimicrobial peptides in Escherichia coli is potentially limited due to their toxicity to host cells and susceptibility to proteolytic degradation, which can be avoided using fusion protein approach. We describe antimicrobial peptide production in E. coli based on forcing antimicrobial peptides into inclusion bodies, which is affective for the production of large quantities of antimicrobial peptides. Chemical reagents for cleaving peptide bond between antimicrobial peptides and fusion proteins such as cyanogen bromide and diluted acid are selective and provide antimicrobial peptides for biological studies in short time. Key words: Antimicrobial peptide, recombinant fusion protein, pET vector, ketosteroid isomerase fusion protein, inclusion bodies, chemical cleavage.

1. Introduction During the past decade, many small cationic antimicrobial peptides have been successfully prepared by recombinant DNA methods (1–7). In contrast to preparation and expression of heterologous proteins in bacteria, as by far the simplest and most inexpensive means to produce large amounts of recombinant protein, expression of antimicrobial peptides faces large potential difficulties because of their cytotoxicity to host cells and sensitivity to proteolytic degradation of nonstructured peptides. Expression systems with an antimicrobial peptide fused to a partner protein are able to avoid those problems because of the reduced


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toxicity against host cells and enhanced product stability since the fusion protein facilitates product recovery and purification (8). Several biological expression systems have been developed by fusing antimicrobial peptides to a partner protein to mask the intrinsic antimicrobial activity of the peptide inside bacterial cells (shown in Table 5.1), and variety of host cells such as bacteria (3, 9, 10), yeast (11), or insect cells (12) have been used. The most commonly used host cell for recombinant protein production is Escherichia coli because of its high growth rate and wellestablished expression system (6). On the other hand, a biological expression system using genetic techniques based on fusion technology is also economically viable for large-scale production. Such fusion proteins generally lack antimicrobial activity if they form insoluble products or tightly interact with antimicrobial peptides. The peptide is released from the fusion by chemical or enzymatic cleavage. Chemical reagents for cleavage of dipeptide between fusion protein and antimicrobial peptide are shown in Table 5.2. Carrier molecules generally take into account the following criteria (13): • The size of the selected carrier molecule should be three to four times larger than that of the expressed peptides of interest. • The isoelectric point of the expressed molecules should be higher or lower than that of the expressed molecule by at least 2 pH units. • There should be a unique chemical or protease cutting site at the interface of fusion partners. • It must not be toxic to the expression host.

Table 5.1 Fusion system used for recombinant antimicrobial protein production Fusion protein partner (5)

Molecular weight (kDa)

pI

Prochymosin (21)

38.0

4.6

Green fluorescence protein (22)

26.8

5.7

Maltose-binding protein (MBP) (23)

44.4

9.2

Ketosteroid isomerase (KSI) (15, 17)

13.7

4.8

Glutatione S-transferase (GST) (14)

15.8

5.3

Thioredoxin (Trx) (24)

11.8

4.6

Intein (25)

35.3

5.3

Baculoviral polyhedrin (26)

28.7

5.8

Ubiquitin (27)

8.5

6.5

Anionic peptide (4)

2.5

3.1

Production of Recombinant Antimicrobial Peptides in Bacteria

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Table 5.2 Chemical cleavage of the dipeptide between fusion protein and antimicrobial peptide Cleavage site

Reagent

Cleavage conditions

Met–X (7)

CNBr

70% TFA, CNBr of 100-fold molar excess over methionyl residues. RT, 24 h

Asp–Pro (15)

HCl or formic acid

90 mM HCl; 85◦ C, 2 h

Asn–Gly (26)

Hydroxylamine

Buffer pH 9.0, 1.7 M hydroxylamine-HCl, 55◦ C, 24 h

Cys–X (28)

NTCB (2-nitro-5tiocyanatobenzoic acid)

20 mM Tris–HCl buffer pH 9.0, NTCB of 20-fold molar excess of the total cysteine content, 37◦ C, 16 h

Although the antimicrobial peptides can be produced via solid-phase chemical synthesis, this method is less suitable to obtain uniformly or selectively isotopically (13 C, 15 N, and 2 H) labeled peptides, which are required to elucidate biophysical properties of the ligand–receptor interaction by high-resolution liquid or solid-state NMR spectroscopy. Recombinant expression of peptides is therefore an alternative to chemical synthesis with the opportunity to incorporate isotopic labels (7, 14). In our laboratory, we have prepared several antimicrobial peptides by recombinant technology. Here, optimized protocol for production of recombinant antimicrobial peptides and selective chemical cleavage from ketosteroid isomerase (KSI) that forms inclusion bodies are described. We describe a protocol for chemical cleavage between fusion protein and antimicrobial peptide using CNBr or acidic cleavage. For this purpose, a Met or Asp-Pro has to be engineered between the fusion partners. The selected strategy of the Asp–Pro cleavage results in an N-terminal proline residue of peptide, which is in fact even favorable for some peptides. We have demonstrated the essential structural role of the N-terminal proline residue for the conformation of antimicrobial peptide adopted in the membrane mimetic environment (15).

2. Materials 1. pET31b(+) (Novagen) (Fig. 5.1), dissolved in sterile MQ. 2. E. coli BL21 (BL3) pLysS (Invitrogen) stored in 15% glycerol at 80ºC.

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Fig. 5.1. Schematic representation of the expression vector pET31(+) which indicates antimicrobial peptides and KSI fusion partner.

3. TB (Terrific Broth) (Sigma) and LB (Luria-Bertani) medium (Sigma): for 1 L LB medium, dissolve 25 g LB mixture in deionized water and autoclave; for 1 L TB medium, suspend 47.6 g TB mixture in 900 mL of deionized water and add 10 g of glycerol (Sigma). Add deionized water to bring volume to 1 L and autoclave for 20 min at 121◦ C. 4. Ampicillin (Sigma): prepare stock solution of 50 mg/mL in sterile MQ water and store in aliquots at –20◦ C. 5. Isopropyl ␤-D-thiogalactoside (IPTG) (Inalco Pharmaceuticals ): prepare 1 M stock solution in sterile MQ water and store in aliquots at –20◦ C. 6. Guanidine-HCl is dissolved at 6 M in MQ water. 7. Hydrochloric acid (Aldrich): prepare 90 mM solution in MQ water. 8. Cyanogen bromide (Aldrich) is stable for months in dry, dark, refrigerated story. Warm to room temperature before opening. Use only white and not yellow crystals. 9. Lysis buffer: 10 mM Tris–HCl pH 8.0, 1 mM EDTA (ethylenediamine tetraacetic acid), and 0.1% DOC (deoxycholate). 10. Wash buffers: wash with 10 mM Tris–HCl pH 8.0, 1 mM EDTA, 0.1% DOC, twice; with 10 mM Tris–HCl pH 8.0, 1 mM EDTA, 0.1% DOC, 2 M urea, twice, and with 20 mM Tris–HCl pH 8.0 three times. 11. Ligation buffer: 20 mM Tris–HCl pH 7.5, 10 mM MgCl2 , 1 mM dithiotreitol.


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12. Digestion buffer: 50 mM potassium acetate, 20 mM Tris– acetate, 10 mM magnesium acetate, 1 mM dithiotreitol pH 7.9.

3. Methods 3.1. Gene Construct Preparation

1. Design the sense and antisense synthetic oligonucleotide encoding the antimicrobial peptides that fuse to the C-terminus of the bacterial ketosteroid isomerase gene. Insertion of coding sequence for peptide is achieved through the recognition site for the restriction endonuclease AlwNI which produces an overhang of three arbitrary nucleotides (in this case methionine coding ATG) bounded on each side by trinucleotide recognition site shown in Fig. 5.2. 2. Denature primers at 95◦ C for 10 min and anneal by slow cooling to the room temperature in the ligation buffer.

Fig. 5.2. (a) Strategy for the construction, production, purification, and CNBr cleavage of ketosteroid isomerase–peptide fusion protein. Oligonucleotides encoding both strands of the antimicrobial peptides were annealed and ligated into the Alw NI site of pET31(+) to create ketosteroid–peptide fusion gene. The gene was placed under the control of T7 lac promotor, which is recognized as a transcription start site by the T7 RNA polymerase additionally controlled by lac repressor. (b) Strategy for the construction, production, purification, and diluted acid cleavage of ketosteroid isomerase– peptide fusion protein.

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3. Pipette into a microfuge tube 1 ␮g pET31b(+), 2 ␮L 10 × digestion buffer, 1 ␮L AlwNI enzyme, and add water to final volume 20 ␮L. Incubate at 37◦ C for 1 h. Take 2–5 ␮L of the digested sample and run on agarose gel to check the result. 4. Mix 100 ng of AlwNI digested pET31b(+) expression vector and synthetic oligonucleotides for antimicrobial peptides with sticky ends in 3:1 molar ratio of insert to vector, 2 ␮L ligation buffer, 1 ␮L T4 DNA ligase; and add water to final volume 20 ␮L and incubate at 16◦ C for 18 h (see Note 1). 5. Transform the ligated plasmid into the DH5 ␣ strain of E. coli as described: • Place competent cells on ice after removing them from the –80◦ C storage. As the cells thaw, add 5 ng of plasmid to 60 ␮L of competent cells. Flick the tubes to mix the contents and store immediately on ice for further 30 min. • Remove tubes from ice and incubate for 4 min in a 42◦ C water bath for a heat shock. Heat shock facilitates the plasmid uptake by bacteria. • Put tubes for 2 min on ice, afterward add 900 ␮L of sterile LB medium to tube and incubate at 37◦ C for 60 min. • Plate 10 ␮L of culture on LB + Amp plate using a glass spreader. Allow the plate to absorb the inoculums for 5 min, then invert and incubate at 37◦ C for 16 h or until colonies grow to the desired size. • Examine the plates and determine the efficiency of ligation and transformation in comparison to the plate of ligation without added insert and identify the colonies harboring the plasmid by PCR using primers KSI (GGCAAGGTGGTGAGCATC) and T7 term (TGCTAGTTATTGCTCAGC) (7). • Isolate the plasmid and determine the nucleotide sequence of the insert. 3.2. Media and Culture Conditions

1. Transform the protein production strain of E. coli BL21 (BL3) pLysS with pET31b(+) encoding KSI-antimicrobial peptide as described in Paragraph 5 in Section 3.1. 2. From a freshly streaked plate, transfer a single bacterial colony to 10 mL LB broth containing ampicillin (100 ␮g/mL). Incubate at 37◦ C overnight in a shaking incubator at 160 rpm. 3. Dilute the overnight inoculums 1:1,000 into the TB broth containing ampicillin and incubate in a shaker at 37◦ C and 220 rpm. 4. Add 0.4 mM IPTG when culture reaches an OD600 of 0.8.


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5. Four hours after induction, centrifuge the bacterial culture at 5,000g force for 10 min and carefully decant supernatant and hold tube, inverted, for several seconds to drain the residual medium. Blot mouth of inverted tube on paper towel to remove any residual medium. 3.3. Purification of the Expressed Proteins and Cleavage from Fusion Protein

1. Suspend the cell pellet in the 10 mL lysis buffer and lyse by ultrasound sonicator in the water bath cooled with ice for 20 min with 3 or 4 s pulses at 50% duty cycle. 2. Centrifuge the bacterial lysate at 15,000g force for 15 min at 4◦ C. 3. Wash the insoluble inclusion bodies with a succession of wash buffers. Centrifuge the mixture at 15,000g force for 10 min at 4◦ C after every wash. 4. Dissolve the insoluble inclusion bodies in 6 M guanidineHCl and centrifuge. 5. Dialyze the soluble supernatant against the deionized water. Centrifuge the precipitate of KSI–peptide fusion protein at 15,000g force for 10 min at 4◦ C (see Note 2). 6. Analyze the produced protein by SDS-PAGE (Fig. 5.3).

Fig. 5.3. SDS-PAGE gel in which lanes 1 and 2 represent total bacterial lysate of noninduced bacteria (1) and bacteria 4 h after IPTG induction (2). Lane 3 represents inclusion bodies after purification.

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3.3.1. Cleavage of the Fusion Protein Containing Met Residue Between the KSI and Peptide

1. Dissolve the dried sample in 70% TFA to a concentration of the fusion protein KSI-antimicrobial peptide of 10 mg/mL. 2. Add cyanogen bromide to the sample solution at 100-fold molar excess over the concentration of methionyl residues in the fusion protein (see Notes 5 and 6). 3. Bubble nitrogen through the solution for 1 min, wrap the flask in aluminum foil to protect from light, and incubate at room temperature for 24 h. 4. Dry the reaction product under vacuum in a rotary evaporator at 30◦ C and wash three times with water and evaporate. 5. Centrifuge the suspension at 15,000g force for 15 min at 4◦ C. 6. Concentrate the soluble antimicrobial peptide with rotary evaporation and analyze with RP-HPLC.

3.3.2. Acid Cleavage of the Asp–Pro Bond Between the KSI and Peptide

1. Asp–Pro bond is acid labile and can be cleaved by incubation at pH < 2. Resuspend the fusion protein in 90 mM HCl 10% (v/v), mix the suspension for 2 h at 85◦ C (see Notes 3 and 7). 2. Neutralize the reaction suspension to natural with NaOH solution. 3. Centrifuge and concentrate the soluble peptide with rotary evaporation. 4. Purify the peptide with HPLC on a C5 RP-HPLC column using a gradient of 5% acetonitrile to 95% acetonitrile and 5 mM HCl (see Note 4). 5. Check the molecular weight of the peptide fractions by mass spectrometer. 6. Typical yield is 15 mg/L of bactericidal culture.

3.4. Production of 15 N-Enriched Recombinant Antimicrobial Peptides

1. Production of 15 N-enriched peptides is performed in M9 minimal medium, where 15 NH4 Cl is used as the sole source of nitrogen. Table 5.3 shows the component of 1 L of the medium for the production of isotope-labeled peptides (see Note 8). The rest of the procedure is the same. 2. Isotope labeling of the recombinant peptide was exacted by MS or NMR.

4. Notes 1. An E. coli expression vector should contain, apart from the gene of interest, an origin of replication, a gene that confers antibiotic resistance, a promoter, and a transcription ter-


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Table 5.3 Components of 1 L of the medium for the production of 15 N-antimicrobial peptide 1. 985 mL of M9-15 N medium, pH 7.4 (autoclaved)

per L

Na2 HPO4 ·2H2 O

7.5 g

KH2 PO4

3.0 g

NaCl

0.5 g

2. 0.5 mL of trace salt (sterile filtered)

per L

CuSO4 ·7H2 O

6.0 g

NaI

0.08 g

MnSO4 ·7H2 O

3.0 g

Na2 MoO4 ·2H2 O

0.2 g

H3 BO3

0.02 g

CoCl2

0.5 g

ZnCl2

20.0 g

FeSO4 ·7H2 O

65.0 g

Biotin

0.2 g

H2 SO4

5.0 mL

3. 1 g 15 NH4 Cl 4. 10 mL glucose (300 mg/L) (sterile filtered) 5. 3 mL 1 M MgSO4 (autoclaved) 6. 2 mL ampicillin (100 mg/mL)

minator. The pET vector system, which is one of the most common expression system used in laboratory-scale cultivations, has an ampicillin resistance which is mostly used only on laboratory scale, because β-lactamase, the enzyme that confers the resistance, degrades ampicillin and thus the selective pressure is lost after a few generations of cell growth. The pET vector system has a T7 promoter, which is transcribed only by T7 RNA polymerase and must be used in a strain carrying a chromosomal T7 polymerase gene which is under the control of a lac promoter (16). The T7 RNA polymerase is under the control of isopropyl ␤-D-thiogalactopyranoside (IPTG)-inducible promoter. We used the pET31b(+) vector (Fig. 5.1), which is designed for cloning and high-level expression of peptide sequences fused with the ketosteroid isomerase protein. Sequence coding for an antimicrobial peptides is subcloned into AlwNI site downstream of the ketosteroid isomerase (KSI) fusion partner. This KSI has been modified to remove all methionine residue in protein (17). Therefore, between the fusion

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protein and antimicrobial peptide we inserted either the residue Met or a dipeptide Asp-Pro, which are unique and allow chemical cleavage between the KSI and peptide. Optimal growth and expression condition for the protein production was established by using TB medium, where the production of the protein was five times higher than in LB medium. 2. Intracellular degradation of mostly unstructured short antimicrobial peptides or its toxicity to host cell is prevented by fusion of peptides to larger proteins. We used a system with ketosteroid isomerase, a protein that is highly insoluble in water as well as in the cytoplasm of bacteria (7). Like all fusion systems that use larger proteins, the absolute productivity of the system is relatively low because of the intrinsic limitation that only small part of the produced recombinant protein is actually the antimicrobial peptides of interest, so that even when fusion protein expression is very high, antimicrobial peptide expression can at best be only moderate (5). In our case approximately 9% of the whole fusion proteins represent antimicrobial peptides. This can be remedied by insertion of peptide concatamers to increase the fraction of the peptide product within the fusion protein (18). Additionally, forcing proteins into inclusion bodies can also be a useful strategy for purification. After cleaning and removal of residues of bacterial wall, we dissolved inclusion bodies in guanidine-HCl, and after dialysis against water more than 90% pure fusion protein is precipitated. Participation occurs rapidly, but we dialyzed the fusion protein overnight to precipitate the maximal quantity of the fusion protein. 3. Peptide bonds of aspartyl residues may be cleaved in diluted acid at rates at least 100 times greater than other peptide bonds, and moreover the aspartyl–prolyl bonds are the most labile of the aspartyl–peptide bonds. An advantage of this type of peptide cleavage is that it is not necessary to solubilize the inclusion bodies in order for this reaction to be effective. Fusion partner (KSI) in this reaction is in insoluble form while the liberated peptide is soluble. Conditions of temperature, incubation time, concentration of hydrochloric acid, and weight/volume concentration of inclusion bodies affect the efficiency of acid hydrolysis. Our results show that optimal conditions for maximal acid cleavage of peptides from fusion protein were achieved at 90 mM HCl in 2 h at 85◦ C and 10% weight/volume concentration of inclusion bodies. In case that the weight/volume concentration of inclusion bodies is increased the reaction rate decreased significantly. The optimal pH for acid hydrolysis is around 1.5–2. Increase


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of the incubation time in 90 mM HCl at 85◦ C above 2.5 h decreased the proportion of the liberated antimicrobial peptides, probably due to the unspecific cleavage the other peptide bonds in the antimicrobial peptide, as shown in Fig. 5.4. The mechanism of action of HCl on Aspcontaining peptides is shown in Fig. 5.5. 4. Traditionally, TFA is used in the mobile phase for RPHPLC separations, because of its effectiveness in solubilizing hydrophobic peptides. However, although it is a volatile component, it remains in sample after drying, suggesting that it is strongly bound to the cationic peptides (19). After an analysis of the product, from the RP-HPLC (Fig. 5.6) column, on the mass spectrophotometer, we detect two products. The molecular mass of the first product corresponds to the peptide, but there is an additional product with the molecular weight increased for a unit of TFA. Since acidic conditions are needed in the hydrophobic steps of purification, we replaced TFA with HCl. Our results demonstrate that the use of HCl as a replacement for TFA in the purification procedure did not affect peptide recovery shown in Fig. 5.7. Moreover, HCl can be removed easily from the sample, while removal of TFA from

Fig. 5.4. Time dependence of peptide cleavage from fusion protein. The fusion protein KSI–antimicrobial peptides was suspended in diluted acid (90 mM HCl) and mixed at 85◦ C to cleave the aspartyl–proline bond between the fusion protein and peptide.

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Fig. 5.5. Mechanism of the cleavage of bonds to the COOH site of aspartyl residues in dilute acid, R1 amino acid residue represents proline.

Fig. 5.6. Reversed-phase HPLC purification of recombinant antimicrobial peptides after HCl cleavage of the KSI–antimicrobial peptide fusion. The peak at 7 min represents purified recombinant peptide.


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Fig. 5.7. Mass spectra of recombinant antimicrobial peptide (theor. 1,299.5 Da) after purification with HPLC.

samples required washing in dialysis membranes by several steps. 5. Note that cleavage at the methionine residues with CNBr depends on pH. In the alkaline pH range, cyanogen bromide reacts with basic groups in proteins, but under neutral and acidic conditions, only methionine and cysteine are attacked by cyanogen bromide. The conditions for cleavage should be mild enough to avoid nonspecific cleavage of other peptide bonds. After cleavage with CNBr, the KSI precipitated in aqueous solution, while the soluble peptide was separated from other contaminants by RP-HPLC. The mechanism of reaction of cyanogen bromide with methionine-containing peptides is shown in Fig. 5.8. 6. In comparison to the method of cleaving peptide bonds with HCl, which is fast and also not toxic, the method to liberate antimicrobial peptides from fusion protein with CNBr takes more time and caution due to its toxicity. Cyanogen bromide is volatile and readily absorbed through the skin or gastrointestinal tract. Therefore, toxic exposure may occur by inhalation, physical contact, or ingestion. It is acutely toxic, causing a variety of nonspecific symptoms. 7. Proteases can also be used to cleave the peptide bond between the fusion protein and antimicrobial peptides but are not always appropriate because some of them leave one or two amino acid residues at the N-terminus of the peptide and cleavage sometimes occurs at site distinct from the enzyme’s nominal specificity (20). Additionally, proteases act

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Fig. 5.8. Mechanism of cleavage of the Met–X bonds by cyanogen bromide.

poorly against insoluble substrates and are sensitive to strong protein solubilizers, such as SDS, TFE, or guanidine-HCl. 8. Note that growth and protein production of bacteria in M9 minimal medium is significantly slower than in complex medium such as LB or TB medium and bacteria take some time to adapt to the growth in the minimal medium. Other procedures in the preparation of isotopically labeled peptides remain identical. References 1. Hara, S. and Yamakawa, M. (1996) Production in Escherichia coli of moricin, a novel type antibacterial peptide from the silkworm, Bombyx mori. Biochem. Biophys. Res. Commun. 220, 664–669. 2. Shen, Y., Lao, X. G., Chen, Y., Zhang, H. Z., and Xu, X. X. (2007) High-level expression of cecropin X in Escherichia coli. Int. J. Mol. Sci. 8, 478–491.

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24. Xu, X. X., Jin, F. L., Yu, X. Q., Ji, S. X., Wang, J., Cheng, H. X., Wang, C., and Zhang, W. Q. (2007) Expression and purification of a recombinant antibacterial peptide, cecropin, from Escherichia coli. Protein Expr. Purif. 53, 293–301. 25. Morassutti, C., De Amicis, F., Bandiera, A., and Marchetti, S. (2005) Expression of SMAP-29 cathelicidin-like peptide in bacterial cells by intein-mediated system. Protein Expr. Purif. 39, 160–168. 26. Wei, Q. D., Kim, Y. S., Seo, J. H., and Cha, H. J. (2005) Facilitation of expression and purification of antimicrobial pep-

tide by fusion with baculoviral polyhedrin in Escherichia coli. Appl. Environ. Microbiol. 71, 5038–5043. 27. Moon, W. J., Hwang, D. K., Park, E. J., Kim, Y. M., and Chae, Y. K. (2007) Recombinant expression, isotope labeling, refolding, and purification of an antimicrobial peptide, piscidin. Protein Expr. Purif. 51, 141–146. 28. Tang, H. Y. and Speicher, D. W. (2004) Identification of alternative products and optimization of 2-nitro-5thiocyanatobenzoic acid cyanylation and cleavage at cysteine residues. Anal. Biochem. 334, 48–61.

Chapter 6 Methods for Building Quantitative Structure–Activity Relationship (QSAR) Descriptors and Predictive Models for Computer-Aided Design of Antimicrobial Peptides Olivier Taboureau Abstract Antimicrobial peptides are ubiquitous in nature where they play important roles in host defense and microbial control. More than 1,000 naturally occurring peptides have been described so far and those considered for pharmaceutical development have all been further optimized by rational approaches. In recent years, high-throughput screening assays have been developed to specifically address optimization of AMPs. In addition to these cell-based in vivo systems, a range of computational in silico systems can be applied in order to predict the biological activity of AMPs for specific bacteria. Among them, quantitative structure–activity relationships (QSARs) method, which attempts to correlate chemical structure to biological measurement, has shown promising results in the optimization and discovery of peptide candidates. Therefore, this chapter is devoted to describe the QSAR method and recent progress applied in AMP. Key words: QSAR, molecular descriptors, antimicrobial peptide design, PLS and machine learning methods.

1. Introduction Antimicrobial peptides (AMPs) constitute a diverse group of compounds that serve a common goal, that is, host organism defense from infection. They are widely distributed in animals, plants, and microbes and are among the most ancient host defense factors. In microbes, they eliminate competing microorganisms occupying the same ecological niches. In higher organisms, they constitute part of the immune system aiding the regulation of endogenous A. Giuliani, A.C. Rinaldi (eds.), Antimicrobial Peptides, Methods in Molecular Biology 618, DOI 10.1007/978-1-60761-594-1 6, © Springer Science+Business Media, LLC 2010

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microbial flora and the response against invading pathogenic microorganisms (1, 2). Due to their antimicrobial properties, these molecules attract practical interest as potential antibiotics for medical and veterinary use. In vitro and in vivo screening systems have been developed in order to optimize the therapeutic effect of specific AMPs (3). Another desirable goal is to develop a computational (or in silico) system capable of automatically evaluating very large compound libraries, thereby limiting the vast sequence space to be screened by these more traditional methods. In silico approaches based on computer-aided design and quantitative structure–activity relationship (QSAR) analysis can rationalize the design of potent therapeutic AMPs (4, 5). The main idea behind QSAR is that any chemical sequence or structure can be described with measured or calculated physico-chemical parameters, also called descriptors, and correlated to their respective biological activity using diverse mathematical models. Then, these models can be used for the prediction of AMP analogs with a potentially higher biological activity (Fig. 6.1). Of course, different aspects have to be taken into consideration in order to develop accurate predictive model. Information about the AMP studied, sequence or structure information, the choice of descriptors, the choice of mathematical model can have some major effect in the accuracy of the QSAR model prediction. Description of the QSAR methods and aspects to consider will be covered in this issue for the design of new AMPs.

2. Materials 2.1. AMP Structure

In general, AMPs range in size from 6 amino acids up to around 60. To date, more than 1,000 different AMPs have been isolated which can be divided into several classes based on bioactivity, structural features, and/or amino acid composition (6). The simplest structures are small, elongated ␣-helical peptides. Other AMPs fold into looped structures, ␤-sheets, or form compact and rigid, disulfide-bridged tertiary structures. Short linear or cyclic amphiphilic peptides that contain both L-amino acids and D-amino acids are also created in synthetic laboratory. To guide lead optimization, high-resolution X-ray crystallography or nuclear magnetic resonance (NMR) structure has been done for some AMPs (3). Knowledge of the spatial location of specific residues as well as the conformation and direction of the side chains can be used in connection with computer-aided design tools and QSAR, to further facilitate rational optimization of the lead backbones.

Methods for Building Quantitative Structure–Activity Relationship Descriptors

Structure

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Biological activity

NMR, Xray or sequence

descriptors related to sequence/structure

QSAR matrix Activity

Descriptor 01

Descriptor 02

Descriptor 03

analogue1

Y1

X01-1

X02-1

X03-1

analogue2

Y2

X01-2

X02-2

X03-2

Regression

Statistical validation Q2, R2

New experimental test

Prediction for new analogues

Mutation which is predicted to optimize the activity

Fig. 6.1. General overview of the material and method in order to develop a QSAR model.

2.2. AMP Biological Activity

Biological activity of AMPs is required to develop QSAR models. A typical biological activity measurement of AMPs is to determine the efficacy of AMP in order to reduce the growth or to kill a microbe. The antimicrobial activity can be determined by measuring the minimal inhibitory concentration (MIC), which is the lowest concentration of AMP that reduces growth by more than 50% after overnight incubation.

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Another activity often considered is the hemolytic activity as AMPs show some blood cell activities as well. Therefore, the lysis of erythrocyte is an activity measurement used also in parallel to the MIC activity. The hemolytic activity can be determined by a “half-maximal effective concentration (EC50 ),” which refers to the concentration of an AMP where 50% of the population exhibits a response. Finally, AMPs are usually not specific to an organism but they have a tendency to show some toxicity to cells (7). Therefore, cytotoxicity assays, based on EC50 , are also used to evaluate the toxicity of AMPs to cells (see Note 1). 2.3. AMP Properties (Descriptors)

To generate a QSAR model, the sequence or preferably the molecular structure of the peptide, using the methods described in Section 2.1, must be described by diverse physico-chemical parameters. Although sequence and structure of AMPs can be very diverse, almost all AMPs are cationic and amphipathic, features that promote interaction with the negatively charged bacterial and fungal membrane. Therefore, these features and parameters related to amphipathicity can be a relevant starting point in the development of QSAR (Fig. 6.2) (8, 9). Basically, the diversity of the descriptors is large. They can be related to not only experimental data such as molecular weight, partition coefficient, or HPLC retention time, but also theory based on the 2D or 3D structure of AMP studied. In this area, the first theoretical descriptors associated with antibacterial and antimicrobial peptides were based on the work of Hellberg et al. (10). They have designed 29 experimental parameters, like the molecular weight, log P, pKa, for each of the 20 natural amino acids and have concatenated them into three parameters, called “z scores,” using a principal component analysis (PCA) (11). The main advantage is that the descriptors are based on the amino acid sequence and the molecular structure is not needed. Taking advantage of the 3D structure information, more complex descriptors can be designed in order to develop more robust QSAR model. Frecer et al. (7). used a combination of 14 descriptors including features such as charge, lipophilicity, and molecular surface area to analyze protegrin analogs. Mee et al. (12). combined more of 1,000 descriptors based on molecular properties to describe a 15-residue cecropin/melittin peptide hybrid (CAMEL 0). More recently, QSAR models based on molecular interaction fields (4) and inductive QSAR descriptors (5) showed promising results. Whereas, the molecular interaction field descriptors intend to mimic the binding energy between the antimicrobial peptides and its environment (represented by atomic probes), the inductive QSAR descriptors are based on the intramolecular steric effects, molecular capacitance,


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Fig. 6.2. Example of descriptors which can be used with Novispirin. (a) Descriptors based on the sequence and amphipathicity. The sequence is represented with a so-called wheel helix. In grey are polar residues and in black nonpolar residues. (b) Based on the AMP structure the surface and volume of hydrophobic area (white) and hydrophilic residue (black) can be computed. (c) Descriptors based on the molecular interaction field of the AMP and probes (defined by atoms). On each grey dot interaction energy between a probe and the AMP is computed.

and electronegativities. It should be noted, both methods are 3Dsensitive and depend on the structure of AMPs (see Note 2).

3. Methods 3.1. QSAR Methods (Linear/Nonlinear)

Historically, the QSAR concept was elaborated by Hammett in the 1940s and Taft in the 1950s. But it became really popular with the work on Hansch in the drug design area in the 1970s. QSAR are considered state-of-the-art methods for prediction of new substrate or new drug in drug design and are routinely used for understanding the relationships between chemical and their biological, pharmacological, and toxicological actions (13). With AMP, it is of relevance to understand how modifications in peptide sequences may lead to better performing drugs and such understanding is possible through mathematical models such as QSAR (see Note 3). To develop such correlation between

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structure and biological activity, many statistical learning methods and multivariate approach can be applied, categorized as linear or nonlinear. 3.1.1. Linear

Linear method was primarily used with AMP (14, 15). In linear method, principal component analysis (PCA), partial least squares projections to latent structures (PLS), and multivariate design are usually associated with each other. Typically, the development of a QSAR model start with the assembling of information, where for a certain set of AMP analogs, biological activity are characterized (defined as Y space) and relevant descriptors reflecting their chemical and structural properties (defined as X space) are associated with each AMP. Such a matrix can be difficult to handle as it is. Therefore, PCA is a mathematical procedure which is able to transform a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components. It is a way to explore the relationships among AMP analogs and among variables. Then the relation between the biological activity and these principal components associated for each AMP can be handled using a PLS regression method. PLS model tries to find the multidimensional direction in the X space that explains the maximum multidimensional variance direction in the Y space. The main advantage of PLS models is the possibility to interpret the influence of the descriptors at the output prediction.

3.1.2. Nonlinear

Recently, QSAR approaches based on nonlinear methods have been used with AMPs. These methods are essentially artificial neural network (ANN) and support vector machines (SVM) (16, 17). ANN is an artificial intelligence which tries to simulate some properties of neural networks. In AMP, ANN involves a network of descriptors which can be defined as input nodes or neurons. These nodes are connected together and form a network which after transformation in a hidden layer sum up into an output node (Fig. 6.3a). SVM is a statistical learning method which minimizes the socalled structural risk in prediction. SVM is essentially used as a classification method, where two classes are separated by a hyperplane (H). The optimized plane is defined as the one that maximizes the margin between the two classes which is measured by the distances between plane H and the planes cutting the nearest sample points on both sides of H, namely, H1 and H2. In particular, the sample points located exactly on planes H1 and H2 are defined as support vectors (Fig. 6.3b). Both methods are considered to give better results, but the interpretation of the models is rather hard and complex compared to linear models (see Note 4).


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Fig. 6.3. (a) Artificial neural network: the input layer represents the descriptors. The hidden layer represents the transformations of the input layer to a reduced level. The output is the final value which can be associated with the AMP considered. (b) Support vector machine: H represents the classification of hyperplane. H1 and H2 hyperplanes are defined by the dots and the crosses which allow the best separation between two classes (also called support vector). The margin width is the distance between the hyperplanes H1 and H2.

3.2. Normalization and Descriptor Selection

In most of the cases, normalization of the descriptor set is recommended for a QSAR analysis. The diversity of descriptors and the scale of values associated with them can be varied from a factor of 1,000 or even more. Therefore, normalization of all the descriptors to a similar scale can help in the accuracy of the model. Some descriptors are not suitable and do not give any information to the model. Some other descriptors are redundant or show a very low variance between each AMP analog. Instead of providing relevant information, they can reduce the quality of the QSAR model prediction. Therefore, in order to remove the noisy variables and improve the predictive abilities of the PLS model, descriptor selection procedure can be performed using methods such as genetic algorithm (GA) or D-optimal design (18). The genetic algorithm is based on the evolutionary theory of Darwin (19). Each AMP is defined by an initial vector (called also initial population) encoding all available descriptors in a bit-string. Then, a new population is generated randomly, covering the entire range of possible solutions. During each successive generation, a proportion of the existing population is selected to breed a new generation. Individual solutions are evaluated through a fitness or cost function before being selected for the next generation. The procedure stops when a solution that satisfies the minimum criteria (usually correlation coefficient or cross-validation) is found. D-optimal design, instead, is more suitable for calibrating linear model. It is an iterative search algorithm which seeks to minimize the covariance of the descriptors estimated for a specified model. This is equivalent to maximizing the determinant D = |X T X| where X is the design matrix of descriptors evaluated at specific treatments in the design space (the set of AMPs). By selecting variables with higher spread and less correlation,

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D-optimal design will conserve more complementary information (20). D-optimal design was used, for example, for a selection of a representative set of cecropin/melittin peptide according to the information spanned in the descriptor space considered. 3.3. Quality Assessment

The quality and the predictive ability of the QSAR models are assessed, in general, with the leave-one-out cross-validation q 2 and the correlation coefficient r 2 (defined also as Pearson correlation coefficient (PCC)) (see Note 5). Matthews correlation coefficient (MCC) is another measure used for the assessment of binary classification. It takes into account the correct class prediction (i.e., active/non-active) and is essentially associated with SVM and ANN methods.

x y x y − n−1 PCC = 2 ( x)2 2 x − n−1 y −

( y)2 n−1

where x is experimental bioactivity, y predicted activity, and n number of data points. (TP × TN) − (FP × FN) MCC = (TP + FP)(TP + FN)(TN + FP)(TN + FN) where TP represents the correct predicted active class (True Positive), TN correct predicted non-active (True Negative), FP is incorrect predicted active class (False Positive), and FN incorrect predicted non-active class (False Negative). Both statistic measurements return a value between –1 and +1, with a perfect prediction at +1. QSAR models with PCC and MCC values above 0.4 are considered to be predictive.

4. Notes 1. Integration of experimental biological activity from different studies of the development of a QSAR model has to be performed with caution. The variation of the protocols and techniques to obtain a biological activity can influence drastically the accuracy of a QSAR model. Instead, a classification model based on SVM, ANN, or PLS-DA can be utilized as it uses a binary system (active/non-active). Nevertheless, consistent biological activity measurement is preferred in the development of a QSAR model.


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2. If the information about the 3D structure of AMPs is available, descriptors which take into account this information, like molecular interaction field descriptors or inductive descriptors, will be favored prior to the sequence or amino acid descriptors. Previous studies have shown that one mutation can change drastically the 3D conformation of an AMP, and 3D descriptors can integrate this information into the QSAR model. 3. Number and diversity of AMP analogs with biological activity are quite important for the development of a QSAR model. The success of this method requires as much information as possible. The majority of the positions in the AMP sequence should be at least mutated to another residue to see their influence on the biological activity. Previous studies have developed QSAR models with 15–20 AMP analogs and it should be the minimum required. 4. Most of the QSAR modeling of AMPs have mainly been successful in designing AMP analogs of the same size. It is still quite challenging to develop such robust models with peptides from highly diverse sizes. However, with the recent advances in high-throughput peptide synthesis and the combination of advanced learning methods like ANN or SVM, QSAR methods should be able to in future studies overcome the size and diversity limitation. 5. Splitting the data set into a training set (for the development of the QSAR model) and a test set for the validation of the model performance is recommended. These models can easily be overtrained, resulting in a very unstable and inaccurate prediction. References 1. Zasloff, M. (2002) Antimicrobial peptides of multicellular organism. Nature 415, 389–395. 2. Mygind, P. H., Fischer, R. L., Schnorr, K. M., Hansen, M. T., Sonksen, C. P., Ludvigsen, S., Raventos, D., Buskov, S., Christensen, B., De Maria, L., Taboureau, O., Yaver, D., Elvig-Jørgensen, S. G., Sørensen, M. V., Christensen, B. E., Kjærulff, S., Frimodt-Moller, N., Lehrer, R. I., Zasloff, M., and Kristensen, H. H. (2005) Plectasin is a peptide antibiotic with therapeutic potential from a saprophytic fungus. Nature 437, 975–980. 3. Raventos, D., Taboureau, O., Mygind, P. H., Nielsen, J. D., Sonksen, C. P., and Kristensen, H. H. (2005) Improving on nature’s defenses: optimization and high throughput

screening of antimicrobial peptides. CCHTS 8, 219–233. 4. Taboureau, O., Olsen, O. H., Nielsen, J. D., Raventos, D., Mygind, P. H., and Kristensen, H. H. (2005) Design of novispirin antimicrobial peptides by quantitative structureactivity relationship. Chem. Biol. Drug. Des. 68, 48–57. 5. Cherkasov, A. and Jankovic, B. (2004) Application of inductive QSAR descriptors for quantification of antibacterial activity of cationic polypeptides. Molecules 9, 1034–1052. 6. Fjell, C. D., Hancock, R. E. W., and Cherkasov, A. (2007) AMPer: A database and an automated discovery tool for antimicrobial peptides. Bioinformatics 23, 1148–1155.

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7. Frecer, V., Ho, B., and Ding, J. L. (2004) De novo design of potent antimicrobial peptides. Antimicrob. Agents Chemother. 48, 3349–3357. 8. Friedrich, C. L., Moyles, D., Beveridge, T. J., and Hancock, R. E. (2000) Antibacterial action of structurally diverse cationic peptides on gram-positive bacteria. Antimicrob. Agents Chemother. 44, 208–209. 9. Tossi, A. (2005) Host defense peptides: roles and applications. Current Protein Pept. Sci. 6, 1–3. 10. Hellberg, S., Sjostrom, M., Skagerberg, B., and And Wold, S. (1987) Peptide quantitative structure-activity relationships, a multivariate approach. J. Med. Chem. 30, 1126–1135. 11. Wold, S., Esbesen, K., and Geladi, P. (1987) Principal component analysis. Chemom. Intell. Lab. Syst. 2, 37–52. 12. Mee, R. P., Auton, T. R., and Morgan, P. J. (1997) Design of active analogues of a 15-residue peptide using D-optimal design, QSAR and a combinatorial search algorithm. J. Pept. Res. 49, 89–102. 13. Dudek, A. Z., Arodz, T., and Galvez, J. (2006) Computational methods in developing quantitative structure-activity relationships (QSAR): a review. CCHTS 9, 213–228.

14. Lejon, T., Strom, M. B., and Svendsen, J. S. (2001) Antibiotic activity of pentadecapeptides modeled from amino acid descriptors. J. Pept. Sci. 7, 74–81. 15. Lejon, T., Stiberg, T., Strom, M. B., and Svendsen, J. S. (2004) Prediction of antibiotic activity and synthesis of new pentadecapeptides based on lactoferricins. J. Pept. Sci. 10, 329–335. 16. Cherkasov, A., Hilpert, K., Jenssen, H., Fjell, C. D., Waldbrook, M., Mullaly, S. C., Volkmer, R., and Hancock, R. E. (2009) Use of artificial intelligence in the design of small peptide antibiotics effective against a broad spectrum of highly antibiotic-resistant superbugs. ACS Chem. Biol. 4, 65–74. 17. Lata, S., Sharma, B. K., and Raghava, G. P. (2007) Analysis and prediction of antibacterial peptides. BMC Bioinformatics 8, 263–273. 18. Gonzalez, M. P., Teran, C., Saiz-Urra, L., and Teijeira, M. (2008) Variable selection methods in QSAR: an overview. Curr. Top. Med. Chem. 8, 1606–1627. 19. Willett, P. (1995) Genetic algorithms in molecular recognition and design. Trends Biotechnol. 13, 516–521. 20. Montgomery, D. C. (2000) Design and Analysis of Experiments (5th ed.). New York: Wiley.

Chapter 7 Synthesis and Thermodynamic Characterization of Small Cyclic Antimicrobial Arginine and Tryptophan-Rich Peptides with Selectivity for Gram-Negative Bacteria Mojtaba Bagheri Abstract One promising strategy to combat the proliferation of bacteria resistance toward current antibiotics is the development of peptide-based drug. Among these compounds is a group of small cyclic peptides rich in arginine (Arg) and tryptophan (Trp) residues with selective toxicity toward Gram-negative bacteria. The small size of these peptides with improved toxicity toward Gram-negative bacteria makes them an interesting candidate to understand the forces responsible for their selectivity and paves the way to develop new therapeutics with potent activity toward multi-resistant Gram-negative bacteria. To reach this goal, isothermal titration calorimetry (ITC) is a useful technique which may provide the complete set of thermodynamic parameters of the interaction of peptides with lipid bilayers mimicking the properties of bacterial membranes within a few hours. The purpose of this chapter is to describe the synthesis of this group of small synthetic antimicrobial peptides together with the application of ITC to study their interaction with lipid membranes. Key words: RW-rich antimicrobial peptides, cyclization, bacterial selectivity, solid-phase peptide synthesis, isothermal titration calorimetry, thermodynamics, unilamelar vesicles.

1. Introduction The development of effective therapeutics for the treatment of infections caused by multidrug-resistant Gram-negative bacteria is a challenge worldwide. Among the available antibiotics those with killing capability against a broad variety of bacterial species and little toxicity toward human tissues are in an urgent need. Due to the non-specific membrane-disturbing mode of action and the absence of immune response, cationic antimicrobial peptides A. Giuliani, A.C. Rinaldi (eds.), Antimicrobial Peptides, Methods in Molecular Biology 618, DOI 10.1007/978-1-60761-594-1 7, © Springer Science+Business Media, LLC 2010

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(CAPs) have become highly attractive as promising therapeutics to overcome bacterial resistance. However, unresolved problems of toxicity against eukaryotic cells, the limited stability against proteolytic digestion in vivo, and high production costs that prevent using them orally and systemically require the development of new classes of CAPs with improved activity profiles (1). One class of CAPs includes those that are rich in particular amino acids like Trp and Arg residues. Tritrpticin and indolicidin as Trp-rich cathelicidin natural antimicrobial peptides (2) or the synthetic hexapeptide Ac-RRWWRF-NH2 identified by screening synthetic combinatorial hexapeptide libraries (3) belong to this group. All these peptides adapt an amphipathic structure in membrane-mimetic environment with hydrophobic residues on one side and charged residues on the other side. Biophysical studies suggest that the charges favor accumulation of the peptides at the negatively charged bacterial membrane surface and the nonpolar face facilitates the penetration of peptides deeper into the cell membrane, leading to membrane destabilization and cell death. Recently, it was shown that introduction of conformational constraints by head-to-tail cyclization of the synthetic hexapeptide RRWWRF distinctly enhanced the selectivity of the sequence toward Gram-negative Escherichia coli. Biophysical studies confirmed that the cyclic peptide is able to permeabilize lipid bilayers (4). However, in contrast to the high antimicrobial activity, the cyclization-related increase in the membrane permeabilizing activity was low. Structural modifications of the cyclic parent peptide demonstrated that single amino acid substitutions or replacement of L-amino acids with D-enantiomers can enhance or abolish the antimicrobial activity toward Gram-negative and/or Grampositive bacteria (5). The sequence diversity and conformational similarity of micelle-bound cyclic hexapeptides and mimetics (6), but different activities, raise the question whether the specific amino acid residues are responsible for the effects or whether the amphipathicity conferred upon the cyclic compounds by the indole and guanidino moiety is sufficient to explain the activity spectra. It seems that not only the charge-driven binding of the peptides at the membranes of E. coli bacteria but also the exact nature of the interaction of aromatic Trp residues at the interface zones of phospholipids in the inner target membrane and the outer lipopolysaccharide layer is important to be understood. To shed light onto this issue, ITC as a technique to study the interaction between the peptides and lipid bilayer mimicking the bacterial membrane is useful. ITC can provide the comprehensive thermodynamic characterization of the binding of antimicrobial peptides to different lipid vesicles (7). The thermodynamic parameters in terms of entropy, enthalpy, and binding constant are useful to understand the mechanism of action of CAPs and their selectivity toward different lipid membranes.

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This chapter includes an efficient protocol for the synthesis of the small linear peptides and their head-to-tail cyclization in solution together with the thermodynamic characterization of the interaction of peptide with different lipid vesicles. To describe the protocol, the highly active antimicrobial peptide, cyclo-RRRWFW with three adjacent aromatic residues was taken as an example (Fig. 7.1). The effect of cyclization is most pronounced for this peptide and it binds strongly to model membranes compared to the less active linear sequence Ac-RRWFWRNH2 . The synthesis protocol can be applied for the synthesis and cyclization of different variety of pharmaceutically interesting sequences (8, 9). For simplification of the thermodynamic characterization of the lipid–peptide interaction by means of ITC, we applied the Langmuir adsorption isotherm to extract the complete thermodynamics profile of the interaction. Based on this assumption that there is one single set of energetically equivalent sites called the “One Set of Sites” binding model, the evaluation and analysis of thermodynamic data was performed.

Fig. 7.1. Chemical structures of linear (A) Ac-RRWFWR-NH2 and (B) cyclo-RRRWFW sequences.

The protocol as described here is turned out to be simple and can be applied to study the interaction of a variety of cell-permeabilizing antimicrobial peptides with vesicles of varying lipid composition to better understand the mode of action of CAPs.

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2. Materials 2.1. Synthesis of Linear and Cyclic Peptides

1. Resins for peptide synthesis: TentaGel S RAM resin, particle size 90 ␮m, capacity 0.25 mmol/g (Rapp Polymere GmbH, Germany) for the synthesis of peptide amide; (2 chloro)-chlorotrityl polystyrene resin, particle size 200– 400 mesh, 1% divinylbenzene, capacity 1.03 mmol/g (Rapp Polymere GmbH, Germany) for the synthesis of peptide acid. 2. Equipments for the synthesis: Shaker (IKA-Labortechnik, Germany), magnetic stirrer (Heidolph, Germany), plastic syringe equipped with a porous frit, mini-membrane vacuum pump (KNF Laboport, Germany), magnetic stir bar, centrifuge (model 5416, Eppendorf, Germany), centrifuge tubes, 100 mL 1-neck round glass flask, Freeze Dryer ALPHA 2-4 LSC (Atr Biotech, Germany), analytical and preparative reversed-phase high-performance liquid chromatography (RP-HPLC) equipments (Jasco, Japan) with reverse phase C18 columns, measuring pipette, electrospray ionization-mass spectrometry (ESI-MS) in the positive ionization mode using an ACQUITY UPLC system with LCT Premier mass spectrometer (Waters Corporation, Milford, MA, USA), rotary evaporator (Heidolph LABOROTA Efficient evaporators; and VACUUBRAND PC3001 VARIO vacuum pump, Germany), UV cell (light path 10 mm), and spectrophotometer (Lambda 9, PerkinElmer, Germany). 3. 9-Fluorenylmethoxycarbonyl (Fmoc)-amino acid derivatives: Fmoc-Arg[2,2,4,6,7-pentamethyldihydrobe- nzofuran-5-sulfonyl (Pbf)]-OH, Fmoc-phenylalanine (Phe)-OH, and Fmoc-Trp[tert-butyloxycarbonyl (t-Boc)]-OH (GLS, China). 4. Peptide cleavage solvents: Trifluoroacetic acid (TFA), dichloromethane (DCM), and diethyl ether (Et2 O). 5. Fmoc cleavage solvents: Dimethylformamide (DMF) and 20% solution (v/v) of piperidine in DMF. 6. Coupling reagent: O-benzotriazol-1-yl-N,N,N ,N tetramethyluronium hexafluorophosphate (HBTU) (IRIS Biotech, Germany). 7. Cyclization reagent: 1-(1-pyrrolidinyl-1H-1,2,3-triazolo [4,5-b] pyridine-1-ylmethylene) pyrrolidinium hexafluorophosphate N-oxide (HAPyU) (3 in Fig. 7.2) (see Note 1). 8. Coupling and cyclization solvents: DMF and N,Ndiisopropylethylamine (DIEA).


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Fig. 7.2. Synthesis of HAPyU.

9. Scavengers: Thioanisole (Fluka, Germany), 1,2ethandithiol (EDT) (Fluka, Germany), and phenol (Honeywell Riedel-de Haen, Germany). 10. Acetylation solvents: Acetic anhydride (Ac2 O) (Fluka, Germany), DIEA, and DMF. 11. Kaiser test solution: Ninhydrin (Sigma-Aldrich, Germany), pyridine (Fluka, Germany), and potassium cyanide (KCN) (Fluka, Germany). Solution A. 2 mL aqueous solution of 1 mM KCN in 98 mL pyridine; Solution B. 5 g ninhydrin in 100 mL EtOH (%5 w/v). 12. Lyophilization solvents: Water and acetonitrile (ACN). 2.2. Thermodynamic Characterization Using ITC

1. Equipments and devices for ITC experiment: Highsensitivity isothermal titration calorimeter (VP-ITC; MicroCal, Northampton, USA), thermovacuum (MicroCal Incorporated, USA, to facilitate thermostatting and degassing samples), 2.5-mL long-needle Hamilton syringe, disposable culture tubes borosilicate glass (KIMBLE GLASS INC. SIZE/CAP 6 × 50 mm, USA), ITC small tubes (for preincubation of the samples and degassing, 2-mL eppendorf vial, measuring pipette and pipette tips, magnetic stir bar (< 10 mm length), and 0.5% Decon in water. 2. Lipid: 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) (molecular mass: 760.1 g/mol) and 1-palmitoyl-2oleoyl-sn-glycero-3[phospho-rac-(1-glycerol)] sodium salt (POPG) (molecular mass: 770.507 g/mol) lipids (Avanti Polar Lipids; Alabaster, Inc., Alabaster, AL, USA) (see Notes 2 and 3). 3. Small unilamelar vesicles (SUVs) preparation: Vacuum pump (∼10–2 to 10–3 mbar) (Leybold TRIVAC, Germany), argon gas source, dynamic light scattering (DLS) on an N4 Plus particle sizer (Beckman Coulter, Fullerton, USA) equipped with a 10-mW helium/neon laser with a wavelength of 632.8 nm at a scattering angle of 90◦ to check the size and polydispersity of the vesicles, titanium-tip ultrasonicator (Labsonic L, B. Braun Biotech, Melsungen; and Sonopuls

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HD 2070, Bandelin electronic, Germany) with clamp, rotary evaporator, cuvettes (polystyrene 10 × 10 × 45 mm) (SARSTEDT, Aktiengesellschaft & Co., Germany), roundbottomed glass tubes (∼10 mL) with lids, volumetric glass pipette, disposal glass pasteur pipette (long form; 230 mm total length), and 2-mL eppendorf vial (for centrifugation). 4. Loading buffer: 10 mM sodium dihydrogen phosphate/ disodium monohydrogen phosphate [(NaH2 PO4 )/ (Na2 HPO4 )], 154 mM sodium fluoride (NaF), pH 7.4 (see Notes 4 and 5). 5. Analysis of raw data: VP-ITC ORIGIN 5.0 (MicroCal Software, Northampton, USA; for baseline correction, peak integration, and adjustment).

3. Methods 3.1. Synthesis of Linear and Cyclic Peptides

The methods outline the synthesis of Ac-RRWFWR-NH2 and cyclo-RRRWFW peptides based on Fmoc/t-Boc strategy. The linear peptide is amidated and acetylated at C and N terminus, respectively. It contains three Arg and three aromatic residues. The cyclic peptide which is the result of ring closure of the unprotected peptide (see Note 6) at the site of Arg and Trp residues positioned at N and C terminus, respectively (see Note 7), has the same number of charges. This is particularly important when the activities of both peptides are compared in terms of the ability to inhibit the growth of bacteria and their affinity toward lipid bilayers.

3.1.1. Solid Phase Synthesis of Linear Peptide

The synthesis of a linear sequence Ac-RRWFWR-NH2 was performed manually by solid-phase peptide synthesis (SPPS). Fmocbased chemistry was used for the preparation of the peptide amide using TentaGel S RAM resin. The synthesis protocol was as follows: 1. Place resin in an appropriate plastic syringe equipped with a porous frit.

3.1.1.1. Peptide Amide

2. Let the resin swell for 30 min after addition of DMF (2 mL DMF for every 100 mg resin). 3. Remove the solvent by filtration under vacuum. 4. Add 20% piperidine in DMF for two times (1 mL of solvent for every 100 mg resin; 5+10 min with agitation) to the vessel to remove the first Fmoc group attached to the resin.


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5. Wash the resin with DMF (1 mL DMF for every 100 mg resin; 5 times for 1 min). 6. Coupling of the first amino acid. Allow 0.5 mmol protected amino acid, 0.5 mmol HBTU, and 1 mmol DIEA in 1.25 mL DMF (for 500 mg resin) to react in reaction vessel while it shakes for 30 min. 7. Wash the resin with DMF (1 mL DMF for every 100 mg resin; 4 times for 1 min). 8. Perform Kaiser test (see Note 8). 9. Remove the Fmoc protecting group of the first-coupled amino acid with 20% piperidine in DMF for two times (1 mL of solvent for every 100 mg resin; 5 + 10 min with agitation). 10. Wash the resin with DMF (1 mL DMF for every 100 mg resin; 5 times for 1 min). 11. Repeat the Steps 4–8 until the completing of the synthesis. 12. Acetylation of the N terminus. Add 3.5 mL DMF, 1 mL Ac2 O, and 0.5 mL DIEA (for 500 mg resin) to the reaction vessel and shake it for about 15 min. 13. Wash the resin with DMF (1 mL DMF for every 100 mg resin; 3 times for 1 min). 14. Wash the resin with DCM (1 mL DCM for every 100 mg resin; 3 times for 1 min). 15. Dry the resin using the membrane vacuum pump for 10 min (before peptide cleavage). 3.1.1.2. Peptide Acid

Use (2 -chloro)-chlorotrityl polystyrene resin for the synthesis of RRRWFW-OH as the precursor of the cyclic peptide (see Notes 9 and 10). 1. Place 500 mg of the resin in a reaction vessel and let it swell with DCM for 30 min (see Note 11). 2. Remove the solvent by filtration under vacuum. 3. First coupling of amino acid. Dissolve 0.5 mmol protected amino acid and 0.5 mmol DIEA in 2.5 mL DCM and add it to the resin and let the mixture agitate on a shaker for 2 h. 4. Drain the vessel. Add 8 mL DCM, 2 mL MeOH, and 1 mL DIEA (v/v/v; 2 times for 10 min) to the vessel to block any unreacted chloro functional group remained on resin (see Note 12). 5. Wash the resin with DCM (1 mL DCM for every 100 mg resin; 5 times for 1 min). 6. Let the resin dry under vacuum.

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7. Quantify the loading of the first amino acid on the resin by UV absorption of the released Fmoc (see Note 13). 8. Coupling of the second amino acid. Follow Steps 4–8 as discussed for the synthesis of peptide amide until the completing of the synthesis. 9. Wash the resin with DCM (1 mL DCM for every 100 mg resin; 3 times for 1 min) and let the resin dry. 3.1.1.3. Cleavage and Deprotection with TFA

Linear peptides are cleaved off from the resin by using TFA containing different compositions of scavengers as follows: 1. Transfer the dried resin (500 mg) to a 100 mL 1-neck round glass flask with a magnetic bar. 2. Add 0.5 g phenol together with addition of 4.25 mL TFA to the glass flask and stir it for 3 h (see Notes 14, 15, and 16). 3. Filter the resin and wash it with TFA followed by DCM (5 mL of solvents for 1 time). 4. Combine the cleavage mixture and subsequent washes and concentrate it under vacuum using the rotary evaporator. 5. Add 50–60 mL Et2 O to the remaining mixture to precipitate the peptide. 6. Transfer the suspended peptide in Et2 O to a tube, centrifuge down the peptide (5,000 × g for 5 min), and let it dry.

3.1.1.4. Lyophilization of Crude Products

1. Transfer the dried peptide to a 100 mL 1-neck round glass flask. 2. Add 4.5 mL H2 O and 0.5 mL glacial acetic acid to the flask in order to dissolve the peptide. 3. Freeze the solution by rotating the round glass flask in a freeze-drying flask at –70 to –80◦ C. 4. Attach the flask to the lyophilizer overnight (see Note 17). 5. Weigh the lyophilized peptide and transfer it to small vial and keep it at –20◦ C.

3.1.2. Peptide Cyclization in Solution

The synthesis of cyclo-RRRWFW is the result of the head-to-tail lactamization of the N and C terminus of the crude peptide acid RRRWFW-OH using HAPyU and DIEA in DMF under dilute condition (see Notes 18–21). 1. Weigh 1 equiv. of dry peptide acid and transfer it into a 100 mL 1-neck round glass flask with a magnetic bar (see Note 22) and dissolve it in appropriate amount of dry DMF to reach a peptide solution with concentration of 5 × 10–4 M. 2. Add 1.1 equiv. HAPyU to the solution with stirring (see Note 23).


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3. Let the cyclization reaction run by addition of 3 equiv. DIEA and stir the mixture for 10 min at room temperature. 4. Transfer a 50 ␮L aliquot of the reaction mixture to an eppendorf vial and dilute it with 100 ␮L of 0.1% TFA in H2 O to stop the cyclization reaction. 5. Check the progress of the reaction with analytical RP-HPLC and/or ESI-MS (see Note 24). 6. Make sure that the reaction has completed and try to remove DMF by the rotary evaporator under vacuum condition. 7. Add 100 mL of H2 O/ACN (4/1 [v/v]) solution to the remaining mixture and freeze-dry it. 3.1.3. Purification and Characterization of the Linear and Cyclic Peptides 3.1.3.1. HPLC

3.1.3.2. Mass Spectrometry

Analytical RP-HPLC performed by using a Jasco HPLC system with a diode array detector operating at four different wavelengths (λ = 220, 280, 301, 360 nm). Runs were carried out on a PolyEncap A 300 (250 × 4.0 mm) column (Bischoff Analysentechnik, Germany). The sample concentration was 1 mg/mL peptide in a solution mixture of 0.1% TFA in 50% ACN in H2 O. The mobile phase A was 0.1% TFA in water, and B was 0.1% TFA in 80% ACN and 20% water (v/v). The retention time (tR ) of the peptides was determined using a linear gradient of 5–95% of mobile phase B over 40 min at room temperature. The purification of crude peptides performed by RP-HPLC using a Shimadzu LC-10A system (Japan) operating at λ = 220 nm using the same eluents with 10 mL/min flow rate. Afterward, the purified peptides are subjected to final lyophilization (see Note 25). ESI-MS was used for further characterization of the peptides. 1. Prepare a stock solution of the peptide of 1 mg/mL concentration in a mixture of 0.1% TFA in 50% ACN in water (v/v). 2. Dilute the sample 10 times in a 1.5-mL eppendorf vial with ultrapure water (Milli-Q Element System, Millipore, Molsheim, France). 3. Centrifuge the vial to get rid of any small particles. 4. Transfer 100 ␮L of the diluted sample into an appropriate vial for ESI-MS. Set the injection volume of sample at 5 ␮L with a flow rate of 200 ␮L/min operating at λ = 220 nm.

3.2. Thermodynamic Characterization Using ITC 3.2.1. Binding Model for Analysis of Data

One simple model to describe thermodynamic profiles of lipid– peptide interaction is the Langmuir adsorption isotherm. In this model, it is assumed that there is limited number of binding sites in a lipid membrane. When the binding sites are energetically equivalent and are made up of n single lipid molecules, it is

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so-called “one set of sites” binding model. This model actually describes the frequently used “chemical equilibrium” term. This model is particularly useful in describing the binding thermodynamics when the number of available binding sites per lipid vesicles is limited, e.g., the interactions between large proteins and the membrane because of steric reasons. However, unlike protein–ligand interactions, the binding of a peptide to a lipid membrane (or a micelle) is best described in terms of a partition equilibrium rather than a stoichiometric binding process. In other words, the solute (i.e., the peptide) can choose between two different phases, namely the aqueous phase (buffer) and the membrane phase (see Note 26). The theory underlying the “One Set of Sites” binding model for a 1:1 stoichiometric interaction is explained below. The following binding equilibriums describe the interaction between lipid and peptide: L+P L.P Ka =

[L .P] [L][P]

[1] [2]

where L is lipid, P is peptide, L.P is the lipid-bound peptide, and Ka is the binding constant. The total concentration of lipid and peptide can be represented by Eqs. [3] and [4] [L]t = [L] + [L .P]

[3]

[P]t = [P] + [L .P]

[4]

and the total heat content of the solution (Q) in the calorimeter cell with a volume (V) is defined by Eq. [5], Q = nθ[P]tΔH ◦ V

[5]

where n is the number of interaction sites in the lipid membrane, θ is the moles of lipids bound per moles of total peptide as shown in Eq. [6], ΔH0 is the heat of binding of the lipid to the peptide. [L .P] [L .P] = [P]t [P] + [L .P] K a [L] K a [L][P] = = [P] + K a [L][P] 1 + K a [L]

θ=

[6]

According to Eq. [6] when there is n number of interaction sites [L .P] = nθ[P]t, and thus, [L] = [L]t − nθ[P]t. On substituting [L] into the Eq. [6] θ is solved as follow:


θ=

[L]t 1 + +1 n[P]t n K a [P]t ⎤

2 1 4[L]t ⎦ [L]t − + +1 − n[P]t n K a [P]t n[P]t 1 2

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[7]

As a consequence, Q can be extracted by combination of the Eqs. [5] and [7] n[P]tΔH ◦ V [L]t 1 Q= + +1 2 n[P]t n K a[P]t ⎤

2 1 4[L]t ⎦ [L]t − + +1 − n[P]t n K a[P]t n[P]t

[8]

Based on this equation, the total heat of content (Q) is the function of ΔH0 , n, and Ka . In an ITC thermogram, the data are plotted as the change in the heat content for each injection (Qi ) of a definite volume of lipid into the calorimeter cell containing a known volume of [L] (Fig. 7.3). With peptide solution versus the molar ratio of [P]t each injection of the lipid vesicle in the titration experiment, some liquid is expelled into the calorimetrically inert access tube by a known volume (ΔVi ). Therefore, the change in the heat released from the ith injection is defined by the Eq. [9]

Fig. 7.3. The raw ITC data (power vs. time) and the integrated data (heat vs. molar ratio) for the injection of (a) POPC (40 mM) and (b) POPC/POPG (3/1 [mol/mol]) (20 mM) SUVs into the calorimeter cell containing linear or cyclic peptide solution (40 ␮M) at 37◦ C. Non-filled circles give the experimental data and the solid line is the result of data fitting based on the non-linear least square analysis with the “one set of sites” binding model. The binding constant (Ka ) for linear and cyclic peptide are KPOPC, linear = 119 M–1 , KPOPC/POPG (3/1), linear = 3.49 × 103 M–1 , KPOPC, cyclic = 1.7 × 103 M–1 , KPOPC/POPG (3/1), cyclic = 1.79 × 104 M–1 .

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ΔQ i = Q i +

ΔVi Q i + Q i − 1 [ ] − Qi − 1 V 2

[9]

The standard free energy of Gibbs (ΔG0 ) for the interaction between the peptide and lipid is related to the binding constant by the Eq. [10]. According to the standard thermodynamic expression shown in Eq. [11], ΔG0 of binding is related to the contribution of the corresponding enthalpy and entropy (ΔS0 ) changes. ΔG ◦ = −RT In[K a (1/M)]

[10]

ΔG ◦ = ΔH ◦ − T ΔS ◦

[11]

Therefore, one can determine the complete thermodynamic profiles of a binding at micromolar level and even smaller by applying the ITC measurement. 3.2.2. Vesicle Preparation 3.2.2.1. Lipid Preparation

1. Weigh a sufficient number of round-bottomed glass tubes with their lids and note them in a lab book before addition of lipid. 2. Add an appropriate volume of lipids dissolved in chloroform to the 10 mL round-bottomed glass tubes using volumetric glass pipette (see Note 27). 3. Remove the solvent by using the rotary evaporator and finally use a high vacuum pump (∼10–2 to 10–3 mbar) overnight and remove traces of chloroform. 4. Put argon over the lipid-containing tubes. Close the tubes with the lids tightly to prevent oxidation of phospholipids. Weigh the closed vials and subtract the weights of the empty tubes to calculate the net weight of the lipid films.

3.2.2.2. Preparation of SUVs

1. Add an appropriate amount of the buffer to the dried lipid and disperse the lipid by shaking and vortexing for 5 min (see Note 28). This will result in a turbid suspension containing large and polydisperse vesicles called multilamellar vesicles (MLVs) (see Note 29). 2. Subject the MLV to ultrasonication in an ice/water bath for 20 min by putting the titanium tip of the ultrasonicator into the lipid suspension. As the result of sonication, the suspension will become clear, which is an indication for the formation of SUVs (see Note 30). 3. Transfer the content of the tube into a 2-mL eppendorf vial and centrifuge it at 7,000 × g for 5 min at 10◦ C to get rid of titanium debris left during the ultrasonication. 4. Transfer the supernatant carefully into another eppendorf vial.


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5. Check the size and polydispersity of the vesicles by DLS (see Notes 31 and 32). 3.2.3. Instrument Setup and Titration Experiment

1. Set the desired temperature for both the calorimeter and the thermovacuum thermostat (e.g., 37◦ C). 2. Prepare a stock solution of peptide at a concentration of 200 ␮M in a 2-mL eppendorf vial in the same buffer as used for the preparation of the lipid solution (see Notes 33 and 34). 3. Prepare a peptide solution (e.g., 40 ␮M) in an ITC small tube by dilution of the stock solution (see Notes 35 and 36). Put a small magnet bar in the tube and place it for at least 5 min in the thermovacuum in order to avoid the formation of bubbles in the calorimeter cell during the titration (see Note 37). 4. Wash the reference and calorimeter cells of the calorimeter with the same buffer used for the experiment for 20 times. Remove the rest of the buffer remained in the cells at the end (see Notes 38 and 39). 5. Wash out the ITC syringe with buffer and if necessary with 5% Decon solution too. 6. Place an appropriate amount of the lipid solution (e.g., 500 ␮L) in a small disposable culture tubes borosilicate glass. Put the ITC syringe into it in order to fill the syringe with lipid solution. Make sure that there are no bubbles inside the ITC syringe by using purge–refill cycles for 2–3 times (see Note 40). 7. Fill the reference cell with the degassed buffer using the long-needle syringe. 8. Fill the calorimeter cell with the degassed peptide solution until it overflows at the top of the cell and avoid the production of bubbles. Then, remove the overflowing solution above the calorimeter cell. 9. Select the instrument setting such as the total number of injections (at least 20), the volume of injection (3– 10 ␮L) (see Note 41), the temperature (as mentioned above), reference power (18 ␮cal/s), initial injection delay (180 s), spacing between injections (300 s) (see Note 42), syringe lipid concentration (20–40 mM), cell peptide concentration (0.04 mM), and stirring speed (310 rpm) (see Note 43). 10. Place the ITC syringe into the calorimeter cell and initiate the titration experiment. If the heats of injection are quite satisfactory, each experiment usually takes 3 h. 11. After the end of the titration experiment, take the ITC syringe out and make the calorimeter cell and ITC syringe

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empty. Wash out the calorimeter cell and ITC syringe completely (see Note 38) and prepare the instrument for the next experiment. 3.2.4. Data Analysis and Fitting

The data are collected based on the program supplied by the manufacturer. Baseline correction, peak integration, and its adjustment for data acquisition and analysis are done using VP-ITC ORIGIN 5.0 software as described by the manufacturer. The raw data were corrected for the heat of dilution of cyclo-RRRWFW and Ac-RRWFWR-NH2 peptides in the buffer (see Note 44). After assuming the values for Ka and ΔH0 , the data fitting is done with the “One Set of Sites” binding model for a 1:1 stoichiometric interaction as described before. According to this model, the data analysis and curve fitting by non-linear least square analysis can be done by VP-ITC ORIGIN 5.0 software. The best fits of the experimental data of the titration of linear and cyclic peptides with lipid vesicles are shown in Fig. 7.3. The fitting program finally gives the values for the binding constant and enthalpy. The entropy and free energy of Gibbs of the system are calculated using Eqs. [10] and [11].

4. Notes 1. HAPyU is the pyrrolidinium derivative of commercially available N-[ (dimethylamino)-1H-1,2,3-triazolo [4,5b] pyridine-1-ylmethylene]-N-methylmethanaminium hexafluorophosphate N-oxide (HATU) (2 in Fig. 7.2) (Sigma-Aldrich, Germany) coupling reagent for peptide synthesis. It is of intermediate stability compared to HATU and can be stored at 0◦ C. It is not hygroscopic and irritating to eyes, the respiratory system, and the skin. It was prepared in our laboratory (10) from 1-hydroxy-7-azabenzotriazole potassium (KOAt) (1 in Fig. 7.2) salt (Fluka, Germany) and commercially available chloro-N,N,N ,N -bis(tetramethylene)formamidinium hexafluorophosphate (Sigma-Aldrich, Germany) using Knorr’s method (11). The molecular mass is 432.31 g/mol. 2. POPC is a zwitterionic phospholipid which is frequently used to mimic the uncharged outer lipid leaflet of mammalian plasma membranes. To mimic the negatively charged inner membranes of Gram-negative bacteria, a mixture of POPC/POPG (3/1 mol/mol) is used. 3. We usually use phospholipids dissolved at concentrations of 20 mg/mL in chloroform. Glass pasture pipettes should be used to handle the solution. The amount of lipid


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transferred to the vials has to be determined gravimetrically after overnight high vacuum evaporation. 4. To prevent any microbial contamination, the buffer should be sterile-filtered and stored at 4◦ C. 5. The heat of protonation and deprotonation of buffer occurring during the interaction between peptide and lipid vesicles can contribute to the heat of binding (ΔH0 ). This can be eliminated by using phosphate buffer. In case of a buffer like tris(hydroxymethyl) aminomethane (TRIS) with a high heat of protonation, it may cause uncertainty for the experimental signals when the heat of protonation of buffer is comparable to that of binding of the peptides to lipid vesicles. 6. One major obstacle for the cyclization of fully protected peptides is their insolubility. One particular example is RRRWFW sequence with two hydrophobic Trp and one Phe residues and three adjacent Arg residues fully protected with bulky and hydrophobic Pbf group. 7. Head-to-tail cyclization of a linear sequence with Arg residue at C-terminal results in ␦-lactam formation instead of the desired cyclic peptide. 8. A few resin beads are placed in a small glass tube and washed with EtOH. Solution A (100 ␮L) together with 100 ␮L of solution B was added via a Hamilton syringe into the glass tube containing the beads. The mixture was incubated at 110◦ C for 5 min. The appearance of a yellow color indicates the complete amino acid coupling. If blue color appears, it is the indication of the presence of free amino groups on the beads. Thus, the coupling procedure has to be repeated. Handling the solution A needs special care as it is very poisonous. Working under a hood and using lab coat, gloves, and glasses are demanded. 9. Other solid supports might be used for the synthesis of peptide acids such as hydroxymethylbenzoic acid (HMBA)-resin, 4-hydroxymethylphenoxyacetyl-4 methylbenzyhydrylamine (HMP)-resin, 4-hydroxymethyl3-methyloxyphenoxybutryic acid (HMPB)-resin, Wang resin, super acid sensitive resin (SASRIN), or TentaGel S AC. The coupling of the first amino acid to these solid supports is usually difficult and sometimes there are risks of low loading of the first amino acid and epimerization of the anchored amino acid chiral center. In contrary, the coupling to (2 -chloro)-chlorotrityl polystyrene resin occurs in a short time and is free of epimerization as it is done without any activated species. However, all the resins mentioned above show the same swelling properties in solvents

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such as DMF or DCM which are usually used for peptide synthesis. 10. One advantage of using (2 -chloro)-chlorotrityl polystyrene resin is the prevention of diketopiperazine formation. The steric constraints of the 2 -chloro group on the resins prevent this problem after anchoring of the second amino acid. 11. The trityl resin is highly moisture sensitive and, thus, the reagents and equipments for the synthesis should be dried before use to prevent hydrolysis of active chloro functional group. 12. As the anchoring of the first amino group via esterification to the resin takes place slowly, the remaining reactive chloride group should be capped. This is particularly important to prevent the synthesis of any side products after loading of the second amino acid. 13. Fill the UV cell with 2.7 mL of 20% piperidine in DMF as a reference solution. Set the UV spectrophotometer at 301 nm. Place the cell into the spectrophotometer and set the instrument to zero. Weigh 5 mg of resin in a 2-mL eppendorf vial, add 1 mL of 20% piperidine in DMF, and agitate the suspension for 20 min. Let the resin settle down. Transfer 100 ␮L of the supernatant to a 1-mL eppendorf vial pre-filled with 900 ␮L of 20% piperidine in DMF. Transfer 300 ␮L of this solution to the UV cell, mix, and measure the absorption for three times. Take the average value and calculate the loading of the first amino acid on the resin according to the Beer–Lambert law 2 × 104 A Loading (mmol/g) = εb where A is absorption, b is width of the UV cell in centimeters, and ε301 = 6,000 M–1 .cm–1 . 14. The Pbf protecting group displays a slow deprotection kinetic with TFA compared to t-Boc. Thus, a longer reaction time is necessary to fully remove the bulky Pbf side chain protecting group, especially here in which three Pbf groups are present. 15. Under these conditions, Trp is still carboxylated and this prevents the transfer of the Pbf group to the indole moiety due to the electron withdrawing property of the carboxylate functionality. The presence of a little amount of water in the cleavage cocktail will facilitate the formation of sulfonated Trp side product. 16. If the Trp residue is used as Fmoc-Trp-OH derivative (without the protecting group), the quality of the crude


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products is significantly influenced by the application of different composition of scavengers. In this case, the application of reagent K is highly recommended. Reagent K is a cocktail as follows: TFA/thioanisole/water/phenol/EDT (82.5/5/5/5/2.5 v/v). It should be pointed out that EDT has a terrible smell and requires careful handling. It is recommended to put all staffs contaminated with EDT such as glass flask, disposal tips, and magnet bar in a dish containing a solution of 10% H2 O2 and 5% KOH overnight and wash it afterward. 17. At this stage, the carboxylate functionality attached to the Trp indole group during the process of cleavage will be removed. 18. Usually, head-to-tail cyclization of peptides containing seven or more amino acid residues takes place without any problem. The cyclization reaction of penta- and hexapeptide is hampered especially in the absence of turn structure inducing amino acids such as N-methyl or D-amino acids. One example is the linear sequence RRRWFW-OH which is discussed in this protocol. In this case, the reaction is either slow or happens with the epimerization of amino acid chiral center at the C terminus. 19. The risk of epimerization and slow rate reactions can be minimized by using HOAt-derived coupling reagents such as HAPyU. In some cases, the reaction proceeds with more than 90% of the desired cyclic product (8). 20. When the linear sequence adopts a conformation which facilitate efficient ring closure, highly concentrated linear precursor can be used (9). 21. As the synthesis of short sequence RRRWFW-OH is easy and done without formation of any deficient sequences, the crude peptide acid may be used for the cyclization reaction without further purification. 22. The lyophilized peptides might contain acetate or TFA salts even after lyophilization for a long time, especially when peptides contain basic amino acid residues such as arginine or lysine. These amounts of residual acetate and TFA salts are usually difficult to quantify. 23. In case of using excess amount of HAPyU, the modification of the amino group present in the sequence to guanidinotype side products is probable (12). 24. Analytical RP-HPLC and ESI-MS can give indications for the progress of cyclization reaction. The retention time of the cyclic peptide usually increases compared to the corresponding peptide acid. In addition, the loss of 18 units in the molecular mass of the linear peptide

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represents the head-to-tail lactamization. (ESI-MS (m/z) [M+H]+ = 988.548). 25. If TFA salt is expected to cause problems either for biological experiments or for thermodynamic studies, it is highly recommended to replace the TFA salt with chloride ion by using a solution of 0.1 N HCl. To do so, dissolve the lyophilized peptide after final purification in 0.1 N HCl solution and freeze-dry it again. 26. The interaction between a peptide and a lipid membrane surface can be described by a two-step model. In the first step, the interaction is initiated by the electrostatic contribution. The second step follows with the hydrophobic interaction causing penetration of the peptide into the hydrophobic core of the lipid bilayer, which will be accomplished by a conformational change of the peptide. In the presence of two immiscible phases such as an aqueous solution (buffer) and the membrane, the membrane-binding peptides which usually carry positive charges distribute between two phases based on their affinity to the phases. This affinity can be described as a partition coefficient and presented as a thermodynamic equilibrium constant. The thermodynamic profiles of the lipid–peptide interaction can be deduced according to this equilibrium. The overall binding constant so-called apparent binding constant (Kapp ) includes both hydrophobic and electrostatic contributions for lipid–peptide interaction and is defined as K app =

Cb γ LCf

[13]

where γ is the bounds of the lipid accessibility factor (1.0 for membrane-permeant solutes, 0.5 or 0.6 for membraneimpermeant solutes interacting with large unilamellar vesicles or SUVs, respectively), Cf is bulk concentration of peptide (unbound peptide), Cb is the concentration of peptide bound to the membrane surface, and L is the total lipid concentration. Depending on the attractive or repulsive nature of the electrostatic adsorption of the peptide on lipid, it will either increase or decrease the peptide interfacial concentration compared to that of bulk solution if the lipid membrane is naturally negative like POPG or neutral like POPC, respectively. If the ratio of lipid/peptide concentration is too low (as usual here in titration of peptide solution with lipid vesicles), this electrostatic contribution cannot be neglected. In the partition equilibrium model, Kapp is corrected for non-specific electrostatic effects to describe the


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partitioning of the peptide between the lipid–water interface and the membrane. This equilibrium is so-called the intrinsic binding constant (K0 ) and described as in Eq. [14] K0 =

Cb γ LCM

[14]

where CM is the interfacial concentration of peptide. The interfacial concentration of the peptide can be related to that of bulk solution according to the Boltzmann equation described in Eq. [15]: CM = Cf exp(−z F0 0 /RT )

[15]

where z is the effective charge number of peptide, F0 is the Faraday constant, Ψ 0 is the membrane surface potential, R is gas constant, and T is the thermodynamic temperature. In consequence, K0 is divided into two parts as shown in Eq. [16] K 0 = K app exp(z F0 0 /RT )

[16]

The value for the Ψ 0 can be calculated from the GouyChapman theory using Eq. [17] based on the membrane surface charge density (σ ): σ 2 = 2,000ε0 εr RT

Ci [exp(−z i F0 0 /RT ) − 1] [17]

i

where ε0 and εr are the electric permittivity of free space and the dielectric constant of water, respectively, zi is the valence of ith species, and Ci is the concentration of the ith dissociated electrolyte in the solution. Finally, σ is obtained according to the theoretical calculation described by Seelig (13), which is corrected for the effect of counterion binding due to the association of Na+ to the POPG headgroups shown in Eq. [18] σ =

Z P e Rb (AL + Rb A P ) (1 + K Na CNa exp(F0 0 /RT ))

Rb =

CP,b γ CL

[18]

[19]

where e0 is the elementary charge (1.602 × 10–9 C), Al is the membrane area occupied by one lipid headgroup (0.68 nm2 ), Ap is the membrane area occupied by the

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peptide (Ap is assumed zero when the peptide adsorbs superficially), Cp,b is the concentration of bound peptide, Cl is the concentration of lipid, KNa is the binding constant of the sodium to the negatively charged lipid headgroup (0.6 M–1 ) with a concentration of CNa . Figure 7.4 shows the data analysis of the interaction between the linear and cyclic peptides with POPC and POPC/POPG (3/1 [mol/mol]) SUVs according to this model.

Fig. 7.4. The calculated surface charge density of lipid and the integrated heat of release versus number of injections for the injection of (a) POPC and (b) POPC/POPG (3/1 [mol/mol]) SUVs into the calorimeter cell containing linear or cyclic peptide solution at 37◦ C. The intrinsic binding constant (K0 ) was derived taking into consideration the electrostatic peptide–bilayer interaction with the Gouy-Chapman theory by using the Excel Solver add-in to fit K0 (14, 15). K0 values for the linear and cyclic peptide are KPOPC, linear = 240 M–1 , KPOPC/POPG (3/1), linear = 1.2 × 103 M–1 , KPOPC, cyclic = 6.7 × 103 M–1 , KPOPC/POPG (3/1), cyclic = 1.2 × 104 M–1 .

27. To have the vesicles composed of different lipid species (e.g., POPC/POPG [3/1 mol/mol]), the different lipids should be dried and weighed one by one in the same vial. 28. The lipid concentration used in ITC experiments depends on the affinity of the peptides for the lipid membranes. The higher the affinity, the lower the minimal lipid concentration. We normally use lipid concentrations at 20–40 mM. For high-affinity peptides, it may be possible to reduce the concentration. 29. MLVs can be stored under argon at –20◦ C for several months. The volume of the lipid suspension should not be less than 1 mL. 30. SUVs are usually less stable. They have to be stored at room temperature under argon and should be used no longer than 3 days. Keeping them at low temperature will result in irreversibly agglomeration.


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31. The average diameter of SUVs is around 30 nm. 32. From a more practical point of view, it is important to note that most proteins and peptides bind to SUVs in an enthalpy-driven way, whereas their interaction with LUVs is mostly dominated by entropy. This means that binding to SUVs can often be easily followed by ITC, whereas binding of the same compounds to LUVs is more difficult to monitor calorimetrically. 33. It is recommended that the purity of the lyophilized peptides is > 95% by analytical HPLC. Small contaminations cause errors in the concentrations and uncertainty in the thermodynamic binding parameters. 34. It is highly recommended to prepare both lipid and peptide solutions in an identical buffer (pH, salt concentration, kind of buffer). Otherwise, the heat of mixing of two different systems will influence the signals of the binding reaction. 35. The calorimeter cell has a volume of 1.3998 mL. To fill up the cell, a larger volume of the sample (∼2.5 mL) is required. 36. The concentration of peptide and lipid should be high enough to ensure complete binding of the injected peptide and to get a reasonable signal. 37. The presence of bubbles in both calorimeter cell and ITC syringe will cause baseline instabilities. 38. Try to wash out the calorimeter cell and/or ITC syringe with 5% Decon followed by at least 30 times washing with the buffer in case you want to run your experiment with another lipid mixture. 39. Try to avoid the cell drying. Otherwise, this can lead to irreversible damage. 40. To have a complete binding isotherm, such as enthalpy, entropy, and free energy of Gibbs, peptide solution has to be placed in the calorimeter cell and lipid vesicles in the ITC syringe. Since, the peptide is titrated with lipid vesicles, it starts with all of the peptide in the aqueous phase, which will then gradually transfer into the membrane phase as the lipid concentration increases in the calorimeter cell. Thus, the ITC peaks will become smaller and smaller because less and less peptide is available in the aqueous phase. This allows not only calculating enthalpy of lipid–peptide interaction, but also the partition coefficient, that is, the preference of the peptide to partition into the membrane phase. If, by contrast, small amounts of the peptide are injected into the lipid vesicle suspension, all signals will be identical.

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Upon each injection, the added peptide will bind completely to the lipid phase thus allowing only the determination of the enthalpy of binding. 41. The ITC signal depends on the concentration of lipid and peptide and the injected volume. Try to modify the injection volume depending on the changes in the heat of the lipid–peptide binding; however, a volume less than 3 ␮L is not recommended. Due to the loss of lipid during the mounting of the syringe and equilibration stage before the actual titration experiment, we usually set the first injection volume to 3 ␮L and do not take the value of its heat of release into account in the data analysis. 42. After each injection, the ITC signal comes back to the signal of baseline. The enthalpy of lipid–peptide binding is measured as the integral of each individual peak. The time between the injections should be long enough to allow the signal returns to the baseline level before the next injection. 43. The speed can be modified to ensure complete mixing of the sample. 44. For the measurement of the heat of dilution, a separate experiment is usually done by injecting the lipid vesicles solution into buffer. Alternatively, we usually consider the average heat of the last injections in a real titration experiment as the effect of heat of dilution.

Acknowledgments Dr. Sandro Keller is gratefully acknowledged with ITC. Dr. Margitta Dathe (FMP) and Professor Michael Bienert (FMP) are thanked for their helpful comments on the manuscript. References 1. Hancock, R. E. W. and Sahl, H. -G. (2006) Antimicrobial and host-defense peptides as new anti-infective therapeutic strategies. Nat. Biotechnol. 24, 1551–1557. 2. Chan, D. I., Prenner, E. J., and Vogel, H. J. (2006) Tryptophan- and arginine-rich antimicrobial peptides: structures and mechanisms of action. Biochim. Biophys. Acta 1758, 1184–1202. 3. Blondelle, S. E. and Houghten, R. A. (1996) Novel antimicrobial compounds identified using synthetic combinatorial library technology. Trends Biotechnol. 14, 60–65.

4. Dathe, M., Nikolenko, H., Klose, J., and Bienert, M. (2004) Cyclization increases the antimicrobial activity and selectivity of arginine- and tryptophan-containing hexapeptides. Biochemistry 43, 9140–9150. 5. Wessolowski, A., Bienert, M., and Dathe, M. (2004) Antimicrobial activity of arginineand tryptophan-rich hexapeptides: the effects of aromatic clusters, D-amino acid substitution and cyclization. J. Pept. Res. 64, 159–169. 6. Appelt, C., Wessolowski, A., Soderhall, J. A., Dathe, M., and Schmieder, P. (2005) Structure of the antimicrobial, cationic hexapeptide cyclo (RRWWRF) and its


7. 8.

9.

10.

analogues in solution and bound to detergent micelles. Chem. Bio. Chem. 6, 1654–1662. Seelig, J. (1997) Titration of lipid-peptide interactions. Biochim. Biophys. Acta 1331, 103–116. Ehrlich, A., Heyne, H. -U., Winter, R., Beyermann, M., Haber, H., Carpino, L. A., and Bienert, M. (1996) Cyclization of allL-pentapeptides by means of 1-hydroxy-7azabenzotriazole-derived uronium and phosphonium reagents. J. Org. Chem. 61, 8831–8838. Ehrlich, A., Rothemund, S., Brudel, M., Beyermann, M., Carpino, L. A., and Bienert, M. (1993) Synthesis of cyclic peptides via efficient new coupling reagents. Tetrahedron Lett. 34, 4781–4784. Bienert, M., Henklein, P., Beyermann, M., and Carpino, L. A. (2002) Uronium/guanidinium salts. In Synthesis of Peptides and Peptidomimetics (4th ed). Goodman M., Felix A., Moroder L., Toniolo C. (Eds.), pp. 555–580, Houben–Weyl

11.

12.

13.

14.

15.

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Methods of Organic Chemistry. Stuttgart: Georg Thieme, Vol. E22a, Chapter 3.8. Knorr, R., Trzeciak, A., Bannwarth, W., and Gillessen, D. (1989) New coupling reagents in peptide chemistry. Tetrahedron Lett. 30, 1927–1930. Albericio, F., Bofill, J. M., El-Faham, A., and Kates, S. A. (1998) Use of onium salt-based coupling reagents in peptide synthesis. J. Org. Chem. 63, 9678–9683. Thomas, P. G. and Seelig, J. (1993) Binding of the calcium antagonist flunarizine to phosphatidylcholine bilayers: charge effects and thermodynamics. Biochem. J. 291, 397–402. Keller, S., Heerklotz, H., and Blume, A. (2006) Monitoring lipid membrane translocatlon of sodium dodecyl sulfate by isothermal titration calorimetry. J. Am. Chem. Soc. 128, 1279–1286. Keller, S., Heerklotz, H., Jahnke, N., and Blume, A. (2006) Thermodynamics of lipid membrane solubilization by sodium dodecyl sulfate. Biophys J. 90, 4509–4521.

Chapter 8 Synthesis of Antimicrobial Peptides Using the SPOT Technique Dirk F.H. Winkler and Kai Hilpert Abstract Developing new lead structures for drugs against multiresistant bacteria is an urgent need for modern medicine. Antimicrobial peptides are a class of drugs that can be used to discover such structures. In order to support development of this research, a fast, easy, and inexpensive method to synthesize peptides is necessary. The SPOT synthesis has the potential to produce the required peptide arrays, synthesizing up to 8,000 peptides, peptide mixtures, or other organic compounds on cellulose or other planar surfaces in a positionally addressable and multiple manner. Protocols for the preparation of cellulose membranes and the SPOT synthesis as well as cleavage of peptides from the support are described. Key words: SPOT synthesis, peptide array, screening, antimicrobial peptides, cellulose membranes.

1. Introduction We are presently facing an era of resistant and multiresistant bacteria, which undermines the success of modern medicine to prevent and treat bacterial infection. As a consequence, there is a great effort to discover new substances for the development of drugs that can treat infections arising from multiresistant bacteria. One promising class of substances is peptides. Some naturally occurring peptides were discovered to possess antimicrobial properties, which gave rise to the term antimicrobial peptides (AMPs). These peptides are active against both Gram-positive and Gram-negative bacteria, fungi, viruses, and parasites (1). In recent years, it has become obvious that AMPs also have an effect on the immune system of mammals (2). For example, they can influence wound A. Giuliani, A.C. Rinaldi (eds.), Antimicrobial Peptides, Methods in Molecular Biology 618, DOI 10.1007/978-1-60761-594-1 8, © Springer Science+Business Media, LLC 2010

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healing, angiogenesis, tissue repair, and the release of cytokines (3). Therefore, these antimicrobial peptides are now also called host defense peptides (HDP). However, it was shown that at least one AMP does stimulate the metastatic phenotype in breast cancer (4). An easy method to synthesize AMPs for an activity screen, preferably with sequences smaller than about 20 amino acids, is the SPOT technology (see Table 8.1). The synthesis requires cellulose membranes set up like filter paper, resulting in a method that is inexpensive and easy to establish in virtually any laboratory (18). Using the SPOT technique, it is possible to synthesize and to screen up to 8,000 peptides, peptide mixtures, or other organic compounds on a letter-size membrane (19 cm × 28 cm) (19–21).

Table 8.1 Recommended literature Description

References

First description of the SPOT technique in detail

(5)

Detailed review regarding synthesis and application of SPOT synthesis

(6)

Protocols for SPOT synthesis using active esters

(7)

Automated SPOT synthesis using HOBt/DIC activation

(8)

Comparison of OPfp and HOBt/DIC activation

(9)

Investigations on the quality of SPOT syntheses

(10)

Characterization of some useful types of filter paper and description of some linkers

(11)

Review about using SPOT synthesis for studying protein–protein interactions

(12)

SPOT synthesis and screening techniques

(13)

SPOT synthesis and screening on living cells

(14)

Peptide libraries synthesized by SPOT technology to develop new antimicrobials

(15)

Investigation of antimicrobial peptides using SPOT technology

(16)

Study of surface-bound antimicrobial peptides on SPOT membranes

(17)

Peptides produced by the SPOT technology can be cleaved from the membrane and directly used in screening for antimicrobial activity (22). Furthermore, the peptides can also be synthesized on modified membranes and their ability to kill bacteria even when tethered to a surface (17). Here, we describe a protocol to synthesize peptides on cellulose membranes and then to subsequently cleave the peptides

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from their support medium. In addition, we also describe the preparation of CAPE and TOTD membranes, which are both suitable for the investigations of tethered peptides.

2. Materials 2.1. Preparation of Cellulose Membranes

1. Solvents: N,N -dimethylformamide (DMF), methanol (MeOH), ethanol (EtOH), N-methylpyrrolidone (NMP), diethylether (DEE), dichloromethane (methylene chloride, DCM), 1,4-dioxane. The quality of solvents for washing steps should be of at least ACS or synthesis grade. Solvents for dissolving reagents must be amine and water free (see Note 1). 2. Homemade membranes for cleavable peptides are prepared from filter paper Whatman 50, Whatman 540, or Chr1 (Whatman, Maidstone, UK) (23, 24) (see Note 2). 3. Amine functionalization of the filter paper by esterification using amino acids: diisopropylcarbodiimide (DIPC, DIC; Fluka), N-methylimidazole (NMI; Sigma), and Fmoc-␤alanine (EMD Biosciences) (see Note 3). 4. CAPE (cellulose-amino-hydroxypropyl ether) membranes: 70% perchloric acid (Alfa Aesar), 2-(bromomethyl)oxirane (epibromohydrine, Fluka), 1,3-diaminopropane (Alfa Aesar), and sodium methylate (sodium methoxide; Fluka). 5. TOTD (trioxa-tridecanediamine) membranes: 70% perchloric acid (Alfa Aesar), epibromohydrine (Fluka), 4,7,10trioxa-1,13-tridecanediamine (Fluka), and sodium methylate (sodium methoxide; Fluka). 6. Staining solution: 0.002% bromophenol blue (BPB; Sigma) in MeOH (20 mg in 1 L).

2.2. SPOT Synthesis of Macroarrays

1. Coupling reagents: diisopropylcarbodiimide (DIPC, DIC; Fluka) and N-hydroxybenzotriazole (HOBt; EMD Biosciences). Coupling reagents are only necessary when preactivated amino-acid derivatives are not used (see Note 4). 2. Nonpreactivated amino acids with protection groups according to the Fmoc-protection strategy (25, 26) (EMD Biosciences and GL Biochem). Preactivated amino-acid derivatives with protection groups according the Fmoc-protection strategy are usually pentafluorophenyl esters (OPfp ester; GL Biochem, EMD Biosciences and Bachem) (27) (see Note 4). 3. Capping solution: 2% acetic anhydride (Sigma) in DMF. 2% Ethyl-diisopropylamine (DIPEA, DIEA; Sigma) can be

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added to deprotonate amino groups and buffer the acetic acid generated during reaction. 4. Deprotection solution A: 90% trifluoroacetic acid (TFA; VWR) (v/v), 5% dist. water (v/v), 3% triisopropylsilane or triisobutylsilane (TIPS or TIBS; Fluka) (v/v), 1% phenol (Sigma) (w/v). 5. Deprotection solution B: 50% TFA (v/v), 3% TIPS or TIBS (v/v), 2% dist. water (v/v), 1% phenol (w/v), 44% DCM (v/v). 1. Ammonia gas (Air Liquide).

2.3. Cleavage from Membrane as Free Peptide Amides

3. Methods If not noted different elsewhere, all washing, incubation, and reaction steps may be performed using a rocking shaker. For the basic cellulose matrix, cut a section of filter paper large enough to accommodate all peptide spots, including controls (see Figs. 8.1 and 8.2). The distance between two spots should be at least 2.8 mm if 0.1 ␮L of coupling solution were used, and at least 8 mm for 1 ␮L spotting volume.

3.1. Preparation of Cellulose Membranes

H N

O

NH2 O

O

β-Ala membrane with β-Ala spacer

OH H N

O

NH2

CAPE membrane OH O

H N

O

O

NH 2

O

TOTD membrane

Fig. 8.1. Structure of different linker types described in this publication.

3.1.1. Preparation of Esterified Membranes

1. Amine functionalization by esterification of filter paper: For functionalization of a membrane with a size of


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Fig. 8.2. Copy of a spot membrane of about a letter size accommodating 450 large spots.

10 cm × 12 cm (size of a 96-well plate) dissolve 0.64 g Fmoc-␤-alanine in 10 mL amine-free DMF. Add 374 ␮L DIC and 317 ␮L NMI. Mix well before transferring this solution into a chemically resistant box with lid. For larger membranes, use proportionally more reagent solution. Place the filter paper of the corresponding size in the box, avoiding air bubbles under the paper, and ensure that the surface of the membrane is slightly covered by the solution. Treat the membrane with the reaction mixture in the closed box for at least 2 h, or overnight (see Note 2). Shaking is not necessary. After the treatment, wash the membrane three times with DMF for at least 30 s each. The membrane can be stored at –80◦ C for several months until needed (see Note 5). For storage, wash the modified membrane at least twice with MeOH or EtOH and air dry in a fume hood or using a hair dryer without heat. 2. Fmoc-deprotection: Treat the membrane twice with 20% piperidine in DMF for at least 5 min each. Wash the membrane at least three times with DMF, followed by washing at least twice with MeOH or EtOH. Duration of each washing should be at least 30 s. 3. Staining (optional) (28) (see Note 6): Treat the membrane with staining solution for at least 2 min until the filter paper shows a homogeneous blue color. If the staining is insufficient, repeat the treatment with fresh staining solution. After staining, wash the membrane at least twice with MeOH or EtOH, until the wash solution remains colorless.

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4. Air dry the membrane in a fume hood or with a hair dryer without heat (see Note 7). The membrane is now ready for the coupling cycle. 3.1.2. Preparation of Cellulose-AminoHydroxypropyl Ether (CAPE) Membranes

Since the membranes can be stored for some time without significant loss of activity, it is efficient to prepare a large membrane (e.g., 18 cm × 28 cm) and then cut it into several smaller membranes if needed. Otherwise, use proportionally less reagent solutions (29). 1. Wash the membrane with about 50 mL of a mixture of 50 mL MeOH and 1 mL 70% aqueous perchloric acid for several minutes. Air dry the membrane. 2. Treat the membrane with 50 mL of a mixture of 5 mL epibromohydrine and 500 ␮L 70% aqueous perchloric acid in 1,4-dioxane. Keep the box closed. After 3 h, wash the membrane once with EtOH or MeOH for about 15 min. 3. Let the activated membrane react overnight with about 60 mL of a 50% solution of 1,3-diaminopropane in DMF. The following day, wash the membrane three times with DMF, twice with water, and then three times with MeOH. 4. After treatment with a methanolic suspension of 5 M sodium methylate, wash the membrane with MeOH (three times), water (five times), and again MeOH (three times). After air drying the membrane is ready to use. The membrane can be stored at –20◦ C for several months until needed. For storage, wash the modified membrane at least twice with MeOH or EtOH and air dry it in the air stream of a fume hood, or using a hair dryer without heat. 5. Staining (optional) (28) (see Note 6): Wash the membrane at least three times with MeOH or EtOH for at least 30 s each. Treat the membrane with staining solution for at least 2 min until the filter paper shows a homogeneous blue color (see Note 8). If staining is insufficient, renew the staining solution. After staining, wash the membrane at least twice with MeOH or EtOH, until the wash solution remains colorless and then air dry the membrane.

3.1.3. Preparation of Trioxa-Tridecanediamine (TOTD) Membranes

The preparation of TOTD membranes follows the same protocol as for the CAPE membranes, with the exception that instead of 1,3-diaminopropane it will use 4,7,10-trioxa-1,13tridecanediamine at Step 3 (30). This membrane is also stable and can be stored at –20◦ C for several months until needed. For storage, wash the modified membrane at least twice with MeOH or EtOH and air dry it in the air stream of a fume hood, or using a hair dryer without heat.


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3.2. SPOT Synthesis of Macroarrays

Peptide synthesis using the SPOT technique can be carried out manually or automated. Manual SPOT synthesis is convenient only for a relatively small number of peptides and a large pipetting volume (>0.5 ␮L). For all other cases, it is recommended to perform the synthesis semi- or fully automated. For synthesis of small spots with a pipetting volume of about 0.1 ␮L spot synthesizers from Intavis AG (Köln, Germany) are very useful (8). If we describe working with amino acids, it always includes the use of other organic building blocks (e.g., PNA monomers, peptoidic elements, heterocycles) (20, 31) those can be used under SPOT synthesis conditions. Here, we describe only the basic procedures for SPOT synthesis of linear peptides. Synthesis of modified peptides, for example, cyclization or side-chain modifications, is described elsewhere in the literature (18).

3.2.1. Preparation of Coupling Solutions

For the preparation of coupling solution containing activated amino acids mostly two different methods were used. First method uses pre-activated Fmoc-protected amino-acid derivatives (e.g., pentafluorophenyl esters). In this approach, only one reagent is necessary, which makes the preparation of coupling solutions very simple and reduces the likelihood of mistakes during the preparation. A disadvantage is the higher price of the amino-acid derivatives. But due to the small amount of activated amino acids used for the synthesis, the absolute cost does not increase significantly. Another disadvantage of this method lies in the fact that activated esters are only commercially available for standard amino acids. For nonstandard amino acids, their preactivated derivatives would need to be synthesized (27), or the second method may be used instead. The second method involves the use of in situ-activated amino acids. Activation of the amino acids is carried out by adding an activator and a coupling reagent to the nonactivated Fmocprotected amino-acid derivative. This method is more time consuming, but can be applied for all building blocks available for use in Fmoc solid-phase peptide synthesis. Method 1: Preparation of 0.3 M solutions with pre-activated amino-acid derivatives. Dissolve most of the amino-acid derivatives in amine-free NMP at a concentration of 0.3 M. Due to poor solubility, the derivative of serine must be dissolved in amine-free DMF. Except for the arginine derivative, the solutions of preactivated amino acids can be used for at least 1 week if the stock solution is stored at or below –20◦ C. Each day, before starting the synthesis cycle, discard the amino-acid solutions of the previous day and replace them with fresh amounts from the stock solutions (see Note 4). Due to the instability of dissolved preactivated arginine derivatives, the solution must be prepared fresh every day.

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Method 2: Preparation of solutions with in situ-activated amino acids or other building blocks. Prepare a 0.9 M solution of HOBt in amine-free NMP. Dissolve the Fmoc-amino acids or desired protected building blocks with the HOBt solution to a concentration of 0.45 M. Except for the arginine derivatives, these solutions can be stored at –20◦ C for at least a week. Use new portions of the prepared amino-acid/HOBt solutions every day (see Note 4). To these solutions, add a freshly prepared mixture of 20% DIC in NMP at a ratio of 3:1 (e.g., for 100 ␮L in situ-activated aminoacid solution mix 75 ␮L HOBt/amino-acid solution with 25 ␮L 20% DIC/NMP) (see Note 9). 3.2.2. SPOT Synthesis of the Peptide Array

1. Definition of the synthesis pattern: Place the dry modified membrane on an inert surface (e.g., stainless steel or polypropylene). Deliver the required volume of activated Fmoc-␤-alanine/DMSO solution to all spot positions (see Note 10). Repeat the delivery after 20 min. 2. Blocking free amino groups on nonspot areas: In order to block the free amino groups on areas surrounding the spot as well as free amino groups on the spot areas those formed no bond to the delivered amino acid, place the membrane face down in a box filled with an appropriate amount of capping solution. Ensure that there are no air bubbles under the membrane. Do not shake! Remove the liquid after about 5 min and add an appropriate amount of a mixture of capping solution with 2% DIPEA. Place the membrane in this solution and allow it to react for about 20 min. 3. Removal of Fmoc-protecting group: Wash with DMF four times for at least 30 s each. Treat twice with 20% piperidine/DMF for 5 min each. Wash again with DMF four times for at least 30 s each. Wash at least twice with MeOH or EtOH. 4. Staining (optional) (28) (see Note 6): Treat the membrane with staining solution in a box while shaking. If the staining solution changes its color to blue very rapidly, renew the solution. Perform the staining until the spots are dyed sufficiently (see Note 11). Wash the membrane at least twice with MeOH or EtOH until the wash solution remains colorless. 5. Dry the membrane in the air stream of a fume hood, or by using a hair dryer without heat (see Note 7). The membrane is now ready for the coupling cycle. 6. Amino-acid coupling: The stepwise build up of peptides starts from the C-terminus. Using the desired volume, deliver the prepared, activated amino-acid solutions to the


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corresponding positions on the membrane (see Note 12). After each delivery cycle, allow the reaction to occur for at least 20 min. To achieve a high coupling yield, it is recommended to repeat the spotting of the activated amino acids at least once. 7. Capping (blocking unreacted free amino groups): Place the membrane face down in a box filled with an appropriate amount of capping solution. Do not shake! Allow the reaction to occur for about 5 min. Remove the liquid. Add an appropriate amount of a mixture of capping solution with 2% DIPEA. Place the membrane in this solution and allow at least 5 min reaction time. 8. Building up the peptide chain: Except for the last coupling cycle, repeat Steps 3–7. For the last coupling cycle, repeat the above steps without capping and staining! 9. Removal of last Fmoc-protecting group: Wash with DMF four times for at least 30 s each. Treat twice with 20% piperidine/DMF for 5 min each. Wash again four times with DMF followed by three times washing with DCM for at least 30 s each. 10. Final side-chain deprotection: Treat the membrane with at least 25 mL of deprotection solution A. For larger membranes, use proportionally more deprotection solutions A and B. The membrane must always be well covered by the deprotection solutions. Keep the box tightly closed. Do not shake. After 30 min, pour off the solution very carefully. Wash the membrane several times with DCM for at least 1 min each; then treat with at least 25 mL of deprotection solution B for 3 h in the closed box without shaking. Pour off the solution very carefully (see Note 13). Wash the membrane at least five times with water for at least 1 min each until the pH value of the washing solution is about 7 (see Note 14). Wash the membrane four times with MeOH or EtOH for at least 1 min each. Dry the membrane in the air stream of a fume hood or with a hair dryer without heat. 3.3. Cleavage from Membrane as Free Peptide Amides

In order to investigate antimicrobial activity of the peptides, it may be necessary to use peptide solutions. In this case, it is necessary to release the peptides from the cellulose membrane. The method described here involves the exposure of the entire dry membrane or the punched-out spots to ammonia gas (see Fig. 8.3). The strongly basic environment breaks the ester bond between the peptides and cellulose by forming a C-terminal amide (see Note 15). The release of peptides with ammonia gas may work only with homemade membranes. Commercially available membranes often have other than ester bonds between functional linker and cellulose. For those membranes, the use of additional

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Fig. 8.3. HPLC image of a Bactenecin-related peptide synthesized via SPOT synthesis and cleaved from the membrane using ammonia.

linkers may be necessary (e.g., thioester (29, 32), HMB linker (33), Rink linker (34, 35)). 1. Place the dry membrane or the punched-out spots in a glass desiccator (see Note 16). 2. Set the desiccator under vacuum. 3. Fill the desiccator with ammonia gas. 4. Repeat Steps 2 and 3 twice. 5. Let it react overnight. 6. On the following day, open the desiccator under a fume hood (Attention! Ammonia gas is highly corrosive and irritant!). Let the gas dissipate over at least 30 min while in the fume hood. 7. If not done before, punch out the spots. Transfer the discs into wells of microtiter plates (MTPs) or into vials in order to dissolve them with the sample buffer (see Note 17).

4. Notes 1. Due to possible degradation under the influence of light, organic solvents, with the exception of MeOH and EtOH, should be stored in the dark. 2. Ready-to-use PEG membranes are available from AIMS Scientific (Braunschweig, Germany). Those membranes are more stable against high TFA concentration and may be treated only with deprotection solution I for 3.5 h.


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3. Due to the flexibility and linear structure of the molecule, ␤-alanine is commonly used for amine functionalization of the filter paper by esterification. Other amino acids can be used (36), but there is a higher risk of losing functionality due to the inherently lower stability of the ester bond between amino acid and cellulose. 4. Reagents must be protected from moisture. To avoid condensation from air humidity, reagent bottles stored in the fridge or freezer should be unopened and warmed up to room temperature for approx. 30 min before use. 5. For longer storage, a loss of loading is possible. Storage of the membranes at –80◦ C is recommended. The membranes can also be stored at –20◦ C or +4◦ C; however, there is a higher risk of losing activity over a long storage period. Before storage, wash the membrane thoroughly. During storage, any traces of amines could lead to a total loss of activity within a short time! In order to proceed with the synthesis after storage, treat the membrane once with DMF for 20 min. 6. The staining has no influence in the synthesis process, but is recommended as test of the completion of the previous coupling step and the presence of free amino groups. A spot or membrane without coupled amino acid and free amino groups would remain white after staining since the amino groups are blocked by the capping step. 7. For faster drying after the washing steps, it is possible to wash the membrane additionally twice with DEE. 8. In contrast to esterified membranes, the dyed background of CAPE and TOTD membranes may disappear only slowly over several coupling cycles. Nevertheless, it does not affect the quality of the synthesis. 9. In order to avoid problems associated with the formation of hardly soluble urea, shake the in situ-activated amino-acid solutions for about 30 min; then centrifuge the mixtures and transfer the supernatant into vials of the synthesis rack. 10. Because of its flexibility and linear structure, ␤-alanine is commonly used for the definition of the spot pattern. It works as a spacer to achieve a distance of the amino functions to the cellulose matrix; however, the distance to the cellulose using TOTD or commercially available PEG membranes (37) is already larger than when ␤-alanine functionalized or CAPE membranes are used (see Fig. 8.1). In both cases, it is unnecessary to use a spacer. The definition of spot pattern can be performed by spotting the activated derivatives of the first C-terminal amino acids of the peptide sequences.

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11. Do not stain the spots too strongly. If the amount of absorbed BPB is too high, some of this dye may be incorporated into the peptide. In that case, removal of the color is difficult and may affect detection after incubation. Due to varying acidity of the coupled amino acids and the builtup peptide chain, differences in the intensity of the staining of the spots are normal (see Fig. 8.2). For example, spots where aspartic acid or cysteine is the last coupled amino acids may show no blue color, whereas arginine and lysine show a strong staining. 12. In order to completely cover the area of large spots, it is recommended to use at least 20% more amino-acid solution volume than in Step 1 of Section 3.2.2. 13. After TFA treatment, the membrane may become very soft. Do not try to lift the membrane out until it becomes harder and less likely to break apart during the washing steps. 14. It is possible to substitute some water-washing steps by washing with PBS or TBS. Nevertheless, after buffer washing the traces of buffer must be removed by washing at least twice with water. 15. If it is necessary to yield a free carboxy terminal, do not treat the membrane with ammonia gas. Instead, treat it with an aqueous basic solution such as ammonium hydroxide or sodium hydroxide solutions (38). Another method to release the peptides is the formation of a C-terminal diketopiperazine. In this case, couple BocLys(Fmoc)-OH instead of the ␤-alanine spacer (Fmoc-␤Ala-OH), followed by coupling of Fmoc-proline as the first coupled amino acid. After TFA treatment, the spots can be punched out and transferred onto a MTP or vials (see Note 10). The peptides will be released by overnight treatment with basic aqueous buffers (pH ≥ 7.5) (5). 16. Many desiccators made from plastics are not inert to ammonia gas; therefore, glass desiccators are strongly recommended. 17. In order to reduce possible contamination with side products from the edge of the spot, the diameter of the punched out membrane discs should be smaller than the spot diameter. References 1. Jenssen, H., Hamill, P., and Hancock, R. E. W. (2006) Peptide antimicrobial agents. Clin. Microbiol. Rev. 19, 491–511. 2. Sørensen, O. E., Borregaard, N., and Cole, A. M. (2008) Antimicrobial peptides in

innate immune responses. Contrib. Microbiol. 15, 61–77. 3. Zhang, L. and Falla, T. J. (2006) Antimicrobial peptides: Therapeutic potential. Expert Opin. Pharmacother. 7, 653–663.

Synthesis of Antimicrobial Peptides Using the SPOT Technique 4. Weber, G., Chamorro, C. I., Granath, F., Liljegren, A., Zreika, S., Saidak, Z., Sandstedt, B., Rotstein, S., Mentaverri, R., Sanchez, F., Pivarcsi, A., and Stahle, M. (2009) Human antimicrobial protein hCAP18/LL-37 promotes a metastatic phenotype in breast cancer. Breast Cancer Res. 11, R6. (Epub ahead of print). 5. Frank, R. (1992) Spot-synthesis: An easy technique for the positionally addressable, parallel chemical synthesis on a membrane support. Tetrahedron 48, 9217–9232. 6. Hilpert, K., Winkler, D. F. H., and Hancock, R. E. W. (2007) Cellulose-bound peptide arrays: Preparation and applications. Biotechnol. Genet. Eng. Rev. 24, 31–106. 7. Kramer, A. and Schneider-Mergener, J. (1998) Synthesis and application of peptide libraries bound to continuous cellulose membranes. Methods Mol. Biol. 87, 25–39. 8. Gausepohl, H. and Behn, C. (2002) Automated synthesis of solid-phase bound peptides. In Peptide Arrays on Membrane Support. J. Koch and M. Mahler (Eds.), pp. 55–68. Berlin, Heidelberg: Springer-Verlag. 9. Molina, F., Laune, D., Gougat, C., Pau, B., and Granier, C. (1996) Improved performances of spot multiple peptide synthesis. Peptide Res. 9, 151–155. 10. Kramer, A., Reineke, U., Dong, L., Hoffmann, B., Hoffmüller, U., Winkler, D., Volkmer-Engert, R., and SchneiderMergener, J. (1999) Spot-synthesis: observations and optimizations. J. Peptide Res. 54, 319–327. 11. Frank, R., Hoffmann, S., Overwin, H., Behn, C., and Gausepohl, H. (1996) Easy preparation of synthetic peptide repertoires for immunological studies utilizing SPOT synthesis. In Peptides in Immunology. C. H. Schneider (Ed.), pp. 197–204. New York: John Wiley & Sons, Ltd. 12. Beutling, U., Städing, K., Stradal, T., and Frank, R. (2008) Large-scale analysis of protein–protein interactions using cellulosebound peptide arrays. Adv. Biochem. Eng. Biotechnol. 110, 115–152. 13. Winkler, D. F. H. and Campbell, W. D. (2008) The spot technique: Synthesis and screening of peptide macroarrays on cellulose membranes. Methods Mol. Biol. 494, 47–70. 14. Otvos, L., Jr., Pease, A. M., Bokonyi, K., Giles-Davis, W., Rogers, M. E., Hintz, P. A., Hoffman, R., and Ertl, H. C. J. (2000) In situ stimulation of a T helper cell hybridoma with a cellulose-bound peptide antigen. J. Immunol. Methods 233, 95–1051. 15. Cherkasov, A., Hilpert, K., Jenssen, H., Fjell, C. D., Waldbrook, M., Mullaly, S. C., Volk-

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mer, R., and Hancock, R. E. W. (2009) Use of artificial intelligence in the design of small peptide antibiotics effective against a broad spectrum of highly antibiotic-resistant superbugs. ACS Chem. Biol. 4, 65–74. Hilpert, K., Elliott, M. R., Volkmer-Engert, R., Henklein, P., Donini, O., Zhou, Q., Winkler, D. F. H., and Hancock, R. E. W. (2006) Sequence requirements and an optimization strategy for short antimicrobial peptides. Chem. Biol. 13, 1101–1107. Hilpert, K., Elliott, M., Jenssen, H., Kindrachuk, J., Fjell, C. D., Körner, J., Winkler, D. F. H., Weaver, L. L., Henklein, P., Ulrich, A. S., Chiang, S. H., Farmer, S. W., Pante, N., Volkmer, R., and Hancock, R. E. W. (2009) Screening and characterization of surface-tethered cationic peptides for antimicrobial activity. Chem. Biol. 16, 58–69. Hilpert, K., Winkler, D. F. H., and Hancock, R. E. W. (2007) Peptide arrays on cellulose support: SPOT synthesis – a time and cost efficient method for synthesis of large numbers of peptides in a parallel and addressable fashion. Nat. Protoc. 2, 1333–1349. Schneider-Mergener, J., Kramer, A., and Reineke, U. (1996) Peptide libraries bound to continuous cellulose membranes: Tools to study molecular recognition. In Combinatorial Libraries: Synthesis, Screening and Application Potential. R. Cortese (Ed.), pp. 53–68. Berlin: Walter de Gruyter & Co. Weiler, J., Gausepohl, H., Hauser, N., Jensen, O. N., and Hoheisel, J. D. (1997) Hybridisation based DNA screening on peptide nucleic acid (PNA) oligomer arrays. Nucleic Acids Res. 25, 2792–2799. Bowman, M. D., Jacobson, M. M., and Blackwell, H. E. (2006) Discovery of fluorescent cyanopyridine and deazalumazine dyes using small molecule macroarrays. Org. Lett. 8, 1645–1648. Hilpert, K. and Hancock, R. E. W. (2007) Use of luminescent bacteria for rapid screening and characterization of short cationic antimicrobial peptides synthesized on cellulose using peptide array technology. Nat. Protoc. 2, 1652–1660. Martens, W., Greiser-Wilke, I., Harder, T. C., ¨ Dittmar, K., Frank, R., Orvell, C., Moenning, V., and Liess, B. (1995) Spot synthesis of overlapping peptides on paper membrane supports enables the identification of linear monoclonal antibody binding determinants on morbillivirus phosphoproteins. Vet. Microbiol. 44, 289–298. Santona, A., Carta, F., Fraghi, P., and Turrini, F. (2002) Mapping antigenic sites of

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Winkler and Hilpert an immunodominant surface lipoprotein of Mycoplasma agalactiae, AvgC, with the use of synthetic peptides. Infect. Immun. 70, 171–176. Fields, G. B. and Noble, R. L. (1990) Solid phase synthesis utilizing 9fluorenylmethoxycarbonyl amino acids. Int. J. Pept. Protein Res. 35, 161–214. Zander, N. and Gausepohl, H. (2002) Chemistry of Fmoc peptide synthesis on membranes. In Peptide Arrays on Membrane Support. J. Koch and M. Mahler (Eds.), pp. 23–39. Berlin, Heidelberg: SpringerVerlag. Atherton, E. and Sheppard, R. C. (1989) Activated esters of Fmoc-amino acids. In Solid Phase Peptide Synthesis – A Practical Approach. A. Giuliani, A. C. Rinaldi (eds.), pp. 76–78. Oxford, UK: IRL Press at Oxford University Press. Krchnak, V., Wehland, J., Plessmann, U., Dodemont, H., Gerke, V., and Weber, W. (1988) Noninvasive continuous monitoring of solid phase peptide synthesis by acid– base indicator. Collect. Czech. Chem. Commun. 53, 2542–2548. Licha, K., Bhargava, S., Rheinlander, C., Becker, A., Schneider-Mergener, J., and Volkmer-Engert, R. (2000) Highly parallel nano-synthesis of cleavable peptide-dye conjugates on cellulose membranes. Tetrahedron Lett. 41, 1711–1715. Ast, T., Heine, N., Germeroth, L., Schneider-Mergener, J., and Wenschuh, H. (1999) Efficient assembly of peptomers on continuous surfaces. Tetrahedron Lett. 40, 4317–4318. Heine, N., Ast, T., Schneider-Mergener, J., Reineke, U., Germeroth, L., and Wenschuh,

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H. (2003) Synthesis and screening of peptoid arrays on cellulose membranes. Tetrahedron 59, 9919–9930. Boisguerin, P., Leben, R., Ay, B., Radziwill, G., Moelling, K., Dong, L., and VolkmerEngert, R. (2004) An improved method for the synthesis of cellulose membrane-bound peptides with free C termini is useful for the PDZ domain binding studies. Chem. Biol. 11, 449–459. Volkmer-Engert, R., Hoffmann, B., and Schneider-Mergener, J. (1997) Stable attachment of the HMB-linker to continuous cellulose membranes for parallel solid phase spot synthesis. Tetrahedron Lett. 38, 1029–1032. Scharn, D., Wenschuh, H., Reineke, U., Schneider-Mergener, J., and Germeroth, L. (2000) Spatially addressed synthesis of amino- and amino-oxy-substituted 1,3,5triazine arrays on polymeric membranes. J. Comb. Chem. 2, 361–369. Rau, H. K., DeJonge, N., and Haehnel, W. (2000) Combinatorial synthesis of four-helix bundle hemoproteins for tuning of cofactor properties. Angew. Chem. Int. Ed. 39, 250–253. Kamradt, T. and Volkmer-Engert, R. (2004) Cross-reactivity of T lymphocytes in infection and autoimmunity. Mol. Divers. 8, 271–280. Zander, N. (2004) New planar substrates for the in situ synthesis of peptide arrays. Mol. Divers. 8, 189–195. Bhargava, S., Licha, K., Knaute, T., Ebert, B., Becker, A., Grötzinger, C., Hessenius, C., Wiedemann, B., Schneider-Mergener, J., and Volkmer-Engert, R. (2002) A complete substitutional analysis of VIP for better tumor imaging properties. J. Mol. Recog. 15, 145–153.

Chapter 9 High-Throughput Screening for Antimicrobial Peptides Using the SPOT Technique Kai Hilpert Abstract The SPOT technique provides a fast, cost-efficient, and highly parallel method to synthesize peptide arrays on cellulose. Peptides synthesized on cellulose can be easily cleaved from the support and used directly in a screening assay for antimicrobial activity. Depending on the equipment, the synthesis and the screening can be performed in a medium- or high-throughput manner. High-sensitivity screening is achieved using a bacterial strain (e.g., Pseudomonas aeruginosa H1001) in which a luminescence-encoding gene cassette has been introduced. The intensity of light produced is directly dependent on the energy level of the bacteria. This screening supports the development of new drugs against multidrug-resistant bacteria. Key words: Screening, antimicrobial peptides, bacteria, yeast, human pathogens, Pseudomonas aeruginosa, luminescence, SPOT, synthesis, peptide array.

1. Introduction With the introduction of sulfonamides in the 1930s, for the treatment of bacterial infections, conventional Western medicine was revolutionized: epidemics caused by bacterial infections were no longer a threat to human kind. In addition, many new medical procedures, including complicated operations such as implants and transplants, became possible when used in conjunction with antibiotics to prevent infection. What we now acknowledge as a standard in modern medicine cannot be achieved without antibiotics, or at the very least not without an unacceptably high risk of infection for the patient. This need for antibiotics is reflected also in its reported usage: in the year 2007 in Germany alone, 250–300 tons of antibiotics were used in human medicine A. Giuliani, A.C. Rinaldi (eds.), Antimicrobial Peptides, Methods in Molecular Biology 618, DOI 10.1007/978-1-60761-594-1 9, © Springer Science+Business Media, LLC 2010

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and 750 tons in veterinary medicine (1). Unfortunately, we now face a new problem: often only a short time after introducing a new antibiotic to the market, resistant bacteria are observed. Today, modern medicine is undermined by multidrugresistant bacteria that can withstand the simultaneous application of several different antibiotics, including such examples as methicillin-resistant Staphylococcus aureus (MRSA), vancomycinresistant Enterococci (VRE), and multidrug-resistant Pseudomonas aeruginosa (2). Without immediate investigation into new substances and treatment strategies, the potential impact of infection by these difficult-to-treat pathogenic bacteria may be devastating. Combinatory chemistry and biological libraries such as phage display are extensively used in efforts to discover new antimicrobial substances (3). Antimicrobial peptides (AMPs), also called host defense peptides, are a class of substances with the potential to treat multidrug-resistant bacteria. Certain naturally occurring AMPs have been selected and intensively studied. For a long time, it was assumed that all AMPs act on the cell membrane to bring about bacterial death; however, it became clear that some of the AMPs seemed to have internal targets and did not damage the membrane (4). The normal approach for studying AMPs was to investigate the antimicrobial activity of naturally occurring peptides against Gram-positive and Gram-negative bacteria, as well as any hemolytic effects and structure–activity relationships. Using this information, a few variants of natural peptides with substitutions were designed and synthesized using standard peptide synthesis. Owing to intensive time, manpower, and cost investments with this standard methodology, only a very few of these variants could be produced and therefore screening hundreds or thousands of peptides for antimicrobial activity is very difficult. In addition, it is also desirable to find short peptide sequences to help to reduce the cost of the new drug. Most of the natural AMPs are longer than 12 amino acids and are too long to be ideal candidates for cost-effective drugs. Peptide synthesis on cellulose can provide an inexpensive, easy-to–use, and time-saving strategy to screen for short peptides with the desired antimicrobial activity. For example, we showed before that screening 1,600 peptides yielding enough information to develop bioinformatics tools, which we then used successfully to screen in silico for highly active peptides against multidrug-resistant bacteria (5, 6). Peptide synthesis by SPOT technology is described in detail in 7 and in this book (8). Around 1,000 peptides can be synthesized on one sheet of cellulose. For each peptide, nine concentration series can be produced and used for tests against nine different bacteria or different isolates of one species. Using two fully automated robots (Intavis AG, Köln, Germany), around 1,800,000 measurements can be performed in 1 year.

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Here we describe the process of screening soluble peptides for antimicrobial activity. A genetically modified P. aeruginosa strain is used to perform a sensitive and easily measurable tool in a highthroughput manner. A bacterial luciferase gene cassette was introduced via a transposon into P. aeruginosa (9). The cassette luxCDABE is comprised of the luciferase itself, as well as enzymes that produce the required fatty aldehyde substrate. The luciferase produces light when reduced flavin mononucleotide (FMNH2 ) and molecular oxygen is provided by the bacteria. Any event that disturbs the energy balance of the bacteria will also disturb the amount of available FMNH2 , which is then registered as a change in light production. The light can be measured sensitively and in a high-throughput manner using a luminescence microtiter plate reader. The method described here already was used for performing substitution analyses of variants of the peptide bactenicin, as well as for a scrambled peptide library and semi-random peptide libraries (5, 10, 11). In principle, this screening can also be performed using unmodified bacteria and standard live/dead staining; however, sensitivity might be strongly reduced.

2. Materials 1. Bromophenol blue (BPB; Sigma). 2. 96-well polypropylene microtiter plates (Corning Inc.). 3. Microseal “F” Foil (BIORAD). 4. 2.1% (wt/vol) Difco Müller–Hinton (MH) broth sterilized by autoclaving (Becton-Dickson). 5. 2.1% (wt/vol) Difco MH broth and 1.5% agar (BectonDickson), sterilized by autoclaving, transferred into Petri dishes (Fisher Scientific). 6. 96-well plates suitable for luminescence (Nunc). 7. 12-channel multipipettor (VWR). 8. Bact. I: 5,000 ␮L MH medium containing 50 ␮L of a H1001 overnight culture. 9. Bact. II: 50 mL sterile 100 mM Tris–HCl buffer, pH 7.3, containing 20 mM glucose and 1920 ␮L H1001 culture (OD600 = 0.35).

3. Methods When planning to synthesize peptides for screening purposes, be aware that for ten peptides, one positive and one negative control peptide also need to be synthesized. Performing this screening

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procedure requires two points to be addressed at the stage of synthesizing peptides using SPOT technology. The first point is that at the last round of the coupling cycle, when the peptides are stained with bromophenol blue, the membrane must be labeled using a pencil to indicate the position of each peptide. For example, a grid can be drawn onto the membrane so that each intersection represents the center of a peptide spot (Fig. 9.1a). The second point, which is critical to successful screening, is that the cellulose membrane must be carefully washed several times with a neutral pH buffer before the peptides are cleaved from the membrane with ammonia gas. When planning the experiment, make sure to address these two points. This protocol is written for peptide spots with a density of 0.5–0.8 mmol/cm2 , and a spot area of approximately 0.25 cm2

A

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Fig. 9.1. Images showing various steps in the screening procedure: (a) Labeled cellulose membrane after synthesis, (b) peptides 1–94, showing all spots labeled directly on the membrane, (c) extract peptide spot 1 using a single hole puncher, (d) transferring the cellulose disk into a well of a 96-well polypropylene microtiter plate, and (e) solubilizing the peptides by adding 200 ␮L of autoclaved distilled water.

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In addition, the antimicrobial activity of the peptide can be investigated in a range of the MIC of inactive ( 3τ ). But if only the first 50 s (t < 3τ ) are fit, τ = 38 s, which is incorrect. For comparison, estimation of the mean lifetime from the half-time with τ = t1/2 /ln2 yields τ = 23.5 s.

ratory (2, 6–9) and uses a numerical approach, whereby theoretical efflux curves are generated from a set of differential equations that represent a particular model, which are then numerically integrated and directly fit to the experimental data. The method deals with partial recovery and non-linear effects, such as aggregation, but is more involved and time consuming. Short of these two methods, for which the reader is referred to the original literature, there is a simple type of analysis that can be performed (14). It does not provide information on the mechanism of the peptide, but it has the advantage that is model independent and provides a quantitative measure of the activity. This latter, simpler method will be described here.

2. Materials 2.1. Synthesis of 7MC–POPE

1. Lipids (Avanti Polar Lipids, Alabaster, AL, USA): 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE).

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2. 7-Methoxycoumarin-3-carboxylic acid-succinimidyl ester (7MC-SE) (Molecular Probes/Invitrogen, Carlsbad, CA, USA). 3. Molecular sieves (Sigma-Aldrich, S. Louis, MO, USA). 4. Potassium carbonate (K2 CO3 ). 5. Organic solvents (HPLC grade): chloroform (CHCl3 ), dichloromethane (CH2 Cl2 ), methanol (MeOH), dimethylformamide (DMF). 6. Zinzade solution: sodium molybdate dihydrate (Na2 MoO4 ·2H2 O), 6.85 g, hydrazine sulfate, 400 mg, sulfuric acid (H2 SO4 ), 250 mL. 2.2. Lipid Large Unilamellar Vesicles (LUVs)

1. Standard buffer: 20 mM MOPS, pH 7.5, 100 mM KCl, 0.1 mM EGTA, 0.02% sodium azide. 2. Carboxyfluorescein buffer: 20 mM MOPS, pH 7.5, 50 mM carboxyfluorescein (Molecular Probes/Invitrogen), 0.1 mM EGTA, 0.02% sodium azide. 3. Phospholipids (Avanti Polar Lipids) in chloroform solutions: 1-palmitoyl-2-oleoyl-sn-glycero-3phosphocholine (POPC), 1-palmitoyl-2-oleoyl-sn-glycero3-phosphoglycerol (POPG), 1-palmitoyl-2-oleoyl-snglycero-3-phosphoserine (POPS).

3. Methods 3.1. Synthesis of 7MC–POPE

The synthesis of 7MC–POPC follows the general method of Vaz & Halmann (15), modified by Gregory et al. (2). The version described here is simpler and more effective. 1. Dry the molecular sieves and K2 CO3 for over 48 h in an oven at 80◦ C (see Note 1). 2. Dry CHCl3 , MeOH, and DMF by pouring them over molecular sieves and leaving in a closed screw-cap tube for 24 h. The volume of the solvent should be only about 2–4 mL larger than the bed volume occupied by the molecular sieves. 3. Lipid (POPE) should be in 10 mol% excess over the probe, that is, a ratio L/P = 1.1/1. Typically 5–10 mg of 7MC-SE is used. The numbers given here assume 10 mg of 7MC-SE (31.5 ␮mol). 4. Pipet the desired amount of POPE (34.65 ␮mol) into a round-bottom flask and rotoevaporate at 60◦ C. Redissolve in a minimal amount of dry CHCl3 (about 700 ␮L) and place in a reaction tube. Use a simple screw-cap tube wrapped in aluminum foil to avoid exposure of the

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fluorophores to light. Place a small magnetic bar into the tube to stir the solution during the reaction. 5. Crush up the required amount of K2 CO3 (in 10 mol% excess over the probe, about 2.5 mg) and add to the reaction tube. 6. Dissolve 10 mg 7MC-SE in about 0.2 mL dry DMF in a separate test tube. 7. Add the 7MC-SE solution dropwise to the reaction tube in the dark. 8. Allow the reaction to stir for about 5 h, monitoring its progress by thin layer chromatography (TLC). 9. The TLC is eluted in a small chamber with CH2 Cl2 /MeOH/H2 O 65:25:4 (v/v/v). The 7MCSE and 7MC–POPE are detected by their fluorescence under a hand-held UV light. POPE is detected by the Zinzade reagent (see Sections 2.1/3.2 and (16)), which stains the phosphate of the headgroup blue (see Note 2). 10. Upon completion of the reaction, the product is isolated by preparative TLC (Analtech, Newark, DE, USA). Spot the product along a straight line about 1 cm to the bottom of the plate and elute in a large chamber with CH2 Cl2 /MeOH 3.5:1 (v/v). Let the plate dry, then elute it again in the same solvent (prepare the solvent anew) for better separation of bands. Keep the plate exposed to minimal light during the entire procedure. Again, detect the product using UV light and Zinzade’s reagent, carefully protecting all of the plate except for a small strip on one side (the Zinzade reagent destroys the probe). 11. Scrape off product band and deposit it in about 10 mL of CH2 Cl2 /MeOH 2:1 (v/v). Filter off silica through a glass Buchner funnel with a fritted disk. 12. Remove the solvent in a rotary evaporator. 13. Redissolve in 4 mL dry CHCl3 . 14. Determine the 7MC–POPE concentration by UV-Vis absorption spectroscopy, in a CHCl3 solution. 7MC– POPE has an absorbance maximum at λ = 348 nm and an emission maximum at λ = 396 nm. The extinction coefficient of 7MC-SE is ε = 2.6 × 104 M–1 cm–1 and that of 7MC (carboxylic acid) is ε = 2.0 × 104 M–1 cm–1 (16). We estimated a similar value, ε = 2.5 × 104 M–1 cm–1 for 7MC–POPE. 3.2. Preparation and Use of the Zinzade Solution

This is a summary of the method described by Kates (17). 1. Dissolve 6.85 g of sodium molybdate (dihydrate) and 400 mg of hydrazine sulfate in 100 mL of deionized water.

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2. Place the molybdate solution on ice and slowly add 250 mL of ice-cold, concentrated sulfuric acid. Allow to cool. 3. Dilute to 1 L with 600 mL of deionized water. This solution can be kept for several months. 4. Place some of the solution in a glass spray bottle. This can be operated with a small rubber bulb or with house air. 5. In a fume hood, place the TLC plate in a cardboard box to reduce contamination of surrounding with sulfuric acid. Spray the TLC plate (partially protected if appropriate) with the Zinzade solution at a distance of about 30 cm. Do not over-wet the TLC. 6. Remove the plate from the cardboard box with forceps and place on a hot plate. Observe the appearance of blue spots corresponding to phosphate groups (phospholipids). Then turn the hot plate to about 200◦ C and allow the TLC plate to ash completely. This eliminates the excess sulfuric acid and leaves the carbon imprint of the compounds on the plate, revealing all non-volatile organic compounds. 3.3. Preparation of Lipid Large Unilamellar Vesicles (LUVs)

1. These instructions are to prepare 1 mL of a 20 mM suspension of LUVs. The volume can be increased as desired for vesicles that do not contain encapsulated dye, but for CFcontaining vesicles it should not exceed 2 mL because that will impair the column separation of vesicles from the external dye. 2. Using a Hamilton glass syringe, pipet 20 ␮mol of lipid (POPC, for example) in chloroform solution, into a roundbottom flask. If the volume is small add about 2 mL of chloroform. To measure peptide binding, include 1–2 mol% 7MC–POPE relative to the total amount of lipid. In this case the vesicles are hydrated with standard buffer. Pre-warm the water bath of the rotary evaporator to 60◦ C. Evaporate on a high rotation speed setting to obtain a thin lipid film on the wall of the flask. Keep under vacuum for 4 h. 3. Hydrate the lipid film by adding 2 mL of standard buffer or CF buffer (see Sections 2.2 and 3.4), as desired (see Note 3). Vortex for about 5 min, making sure to place the vortex plate directly under the film and rotating the flask to get the lipid off the wall of the flask. This procedure produces a turbid suspension of multilamellar vesicles (MLVs). 4. If this is a preparation of vesicles with encapsulated CF, the extent of dye encapsulation can be enhanced by subjecting the MLVs to five freeze–thaw cycles (see Note 4). 5. Extrude the MLV suspension 10 times with an extruder (Lipex Biomembranes, Vancouver, Canada) through two stacked polycarbonate filters of 0.1 ␮m pore size (e.g.,


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Nuclepore, from Whatman, Florham, NJ, USA) at a temperature above the Tm of the lipid. This produces LUVs of about 100 nm in diameter. 6. If this is a preparation of vesicles with encapsulated CF, the hydration is done with CF buffer in Step 3. In this case, the CF in the external medium must be separated from the vesicles. This separation is achieved with a small (30 cm) column of Sephadex G-25 (Sigma-Aldrich) equilibrated with standard buffer. Collect 2 mL fractions. The vesicles will elute close to the void volume of the column, and will not be fluorescent because of self-quenching, but are easily detected by the eye because of turbidity. In the end, the CF that remains adsorbed to the column can be eluted with 50 mM KOH. 7. Determine the lipid concentrations using the standard method of Bartlett (18) or one of its modified versions (6). 3.4. Preparation of Carboxyfluorescein Buffer

1. CF is only soluble in aqueous solutions when it is fully deprotonated. Therefore, the pH needs to be 7.5 or higher (if this is a problem, use calcein instead of CF). 2. Prepare a buffer identical to the standard buffer but without any KCl (see Note 5). 3. Mix the CF powder with the buffer and titrate the solution with concentrated (about 1 M) KOH under the pH meter, until all the CF is dissolved and the pH is 7.5 (see Note 6). Then bring up to the desired volume with buffer (without KCl). 4. Filter the CF buffer through a syringe filter with 0.2 ␮m pore size (Whatman 25 mm GD/X, NYL) (see Note 7). 5. Store the CF buffer in the refrigerator.

3.5. Carboxyfluorescein Efflux Kinetics

1. The efflux of CF as a function of time, induced by peptide interaction with the lipid vesicles, is measured in a stoppedflow fluorimeter (see Note 8). We have used the SX-18MV instrument from Applied Photophysics (Leatherhead, UK), but other companies make alternative, high-quality instruments (Bio-Logic, Claix, France and KinTek, Austin, USA, for example). 2. Identical volumes of 1–2 ␮M peptide solutions are mixed with vesicle suspensions of 50–1,000 ␮M in lipid, in the stopped-flow system, to produce final concentrations that are one-half of the original ones. The excitation is at λ = 470 nm (the CF maximum is actually at 490 nm) and the emission at 520 nm. In the absence of a second monochromator, the emission can be recorded through a long-pass filter (e.g., OG 530, Edmund Industrial Optics, Barrington, NJ, USA).

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3. The final CF release has to be normalized to the maximum possible release from the vesicles. This maximum fluorescence is obtained by adding the detergent Triton X-100 to the vesicles, to a final detergent concentration of 1% (of the aqueous solution). All dye is released under these conditions (see Note 9). 3.6. Measurement of Peptide Binding to LUVs

1. Prepare a peptide solution of 1–2 ␮M and a series of about 8–10 vesicle suspensions with lipid concentrations varying from 50 to 800 ␮M. After mixing in the stopped-flow system, these concentrations will be halved. 2. The kinetics of association of peptide with LUVs are recorded in a stopped-flow fluorimeter (e.g., SX.18MV from Applied Photophysics) measuring the increase in FRET from the Trp of the peptide to 7MC–POPE. Trp is excited at 280 nm and the emission of 7MC is measured at 396 nm or through a GG-385 cut-off filter (Edmund Industrial Optics) (see Note 10). 3. Record the fluorescence emission of 7MC–POPE, which increases as a function of time, as more peptide binds to the vesicles (Fig. 11.3a) (see Note 11). 4. To obtain the on- and off-rate constants (see analysis below at Section 3.7) perform this experiment as a function of lipid concentration, from about 25 to 400 ␮M (final lipid concentrations, after mixing). Record about 10 repeats (at least triplicates) for each curve. If the signal-to-noise ratio is poor, it is necessary to acquire more traces and average of about 10–20 to improve the signal/noise ratio (see Note 12).

3.7. Analysis of Peptide Association Kinetics

1. Fit the experimental binding kinetic curves with a single exponential rising function (Fig. 11.3a). Extract the value of the apparent rate constant kapp , which is related to the molecular on- and off-rate constants for binding to the vesicles by kapp = koff + kon [L], where [L] is the lipid concentration. 2. Since the experiments were performed for various lipid concentrations, now plot kapp against the lipid concentration. This yields a straight line, with slope kon and y-intercept koff (Fig. 11.3c). 3. The equilibrium dissociation constant is obtained by KD = koff /kon .

3.8. Analysis of Dye Efflux Kinetics

1. The most straightforward method is to calculate the mean lifetime (τ ) of efflux numerically (14). First, differentiate the CF efflux curve (Fig. 11.5 ), F(t), numerically to obtain its derivative F(t). This function is the probability density


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function. Second, evaluate τ by integration between time zero and the completion time of the curve, according to equation [1] (see Note 13): τ=

t F (t)dt/

F (t)dt

2. A simpler, albeit less satisfactory, alternative to the calculation of the mean lifetime by equation [1] is to fit the CF efflux curves with the smallest number of exponential functions needed to obtain a very good fit (Fig. 11.5). Typically 2 or 3, but rarely more than 3 exponentials are required. The lifetime is then obtained by an amplitude-weighted average of the characteristic time constants (τ i ) of each exponential. For example, for 2 exponentials, bring the origin of the experimental F(t) to zero, and fit the curve with the function f(t) = Ao [1–α 1 exp(–t/τ 1 )–α 2 exp(–t/τ 2 )], with α 1 + α 2 = 1, and where Ao is a global amplitude factor. The lifetime is then given by τ = α 1 τ 1 + α 1 τ 2 . The apparent rate constant for efflux is the reciprocal of τ (see Note 14).

4. Notes 1. Exclusion of water both from solvents and reactants is the essential condition for a successful synthesis. Hence, the need to dry all solvents and K2 CO3 . K2 CO3 is the base in the reaction, which is necessary to keep the nucleophile (the amino group of the ethanolamine headgroup) in the deprotonated state (–NH2 ). 2. The 7MC–POPE spot should be the only spot on the TLC that is detected both by fluorescence and the Zinzade solution. Approximate Rf s are POPE, 0.53; 7MC–POPE, 0.76; and 7MC-SE, 0.92. 3. The buffer must be at a temperature higher than the phase transition temperature of the lipid (Tm ). For POPC Tm is –4◦ C, so room temperature is appropriate, but if saturated lipids are used, care must be taken to ensure that the buffer temperature is higher than Tm . 4. The freeze–thaw procedure also helps eliminate small vesicles, which fuse with larger ones, and could otherwise result in artifacts in the peptide-induced dye release kinetics. 5. The osmolarity of the CF buffer solution will be equivalent to the osmolarity of the standard buffer, as the contribution

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of CF and its counter ions will be equivalent to that of 100 mM KCl. 6. Be careful not to overtitrate, as this will cause an imbalance in the osmotic strength compared to standard buffer. 7. This step is essential to remove any undissolved material, which will clog the filters during extrusion. 8. If the efflux is slow, typically longer than 1,000 s for completion, the curves can be recorded in a steady-state spectrofluorimeter, by adding the peptide solution to the vesicle suspension in the cuvette. The initial value must be measured prior to peptide addition, and the Triton X-100 release level is determined in the same sample by adding detergent, to a concentration of 1%, at the end of the experiment. If the efflux occurs in a time longer than 1 s but shorter than about 20 s, measurement in the cuvette is very inaccurate. In the absence of a stopped-flow instrument, it is possible to use a rapid kinetics accessory (e.g., RX2000 from Applied Photophysics) that is mounted on the steadystate fluorimeter. 9. The Triton X-100 release level can also be determined separately, in a steady-state spectrofluorimeter [we have used the 8100 SLM-Aminco (Urbana, IL, USA) instrument, upgraded by ISS (Urbana, IL, USA), or the Jobin-Yvon (Edison, NJ, USA) instruments Fluorolog and Fluoromax], by measuring the initial fluorescence, before adding detergent, and the final fluorescence, after detergent addition. The initial fluorescence value is necessary to convert the measurements in the two experiments (stopped flow and steady state) to a common scale. 10. FRET between an intrinsic Trp residue of the peptide and 7MC–POPE incorporated in the lipid membrane is used to monitor peptide binding. If the peptide is bound, instead of emitting fluorescence at 320–350 nm, it transfers its excitation energy to 7MC–POPE, which absorbs maximally at 348 nm. The fluorescence emission maximum of 7MC–POPE occurs at 396 nm. In order for FRET to occur, the Trp residue and the 7MC fluorophore need to be approximately within the Förster distance. For ˚ if this pair of fluorophores, the Förster distance is 26 A the Trp emission maximum is at about 330 nm, but the ˚ depending on the waveexact value may vary by 1–2 A, length of the Trp emission maximum, which is determined by its physical environment. The distance for transfer from Trp to other coumarin fluorophores, such as 7hydroxycoumarin (6) and methylcoumarin (19), is similar ˚ (25 A).


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11. Binding is monitored typically for less than 1 s, sometimes less than 0.1 s. Many antimicrobial and cytolytic peptides induce other, post-binding changes in the vesicles that also result in fluorescence changes, which should not, however, be mistaken for binding. 12. If binding is very tight, it may be necessary to perform a different experiment to obtain a good estimate of the off-rate constant. In this case, peptide (about 1 ␮M) is preincubated with vesicles (about 100 ␮M) that contain the lipid probe (7MC–POPE), which are then mixed in the stopped-flow system with an excess of vesicles (about 1 mM) that do not contain any probe. Binding to the acceptors can be made quasi-irreversible by changing their lipid composition. For example, many antimicrobial peptides are cationic and therefore bind much better to anionic vesicles. In this case, one would prepare acceptor vesicles with a higher content of anionic lipids (such as POPG) than present in the donor vesicles. Peptide will now dissociate from the donor vesicles and will bind to the acceptor vesicles, leading to a decrease in fluorescence of 7MC–POPE from the donors (Fig. 11.3b ). 13. This analysis of efflux curves does not allow for inferences regarding the peptide mechanism but can be used with confidence to compare the peptide activity as a function of lipid concentration, vesicle, composition, temperature, etc. Calculating the average lifetime is far superior to using initial rates of efflux, which take into account only a small portion of the curve, discarding the majority of the data points. Using initial rates also overlooks the problem that the shapes of curves vary considerably, leading to erroneous results. For example, sigmoidal curves (Fig. 11.5), which exhibit an initial lag time, will produce low initial rates of efflux, but often this is more than compensated by a sudden increase in peptide activity after the lag. For the numerical differentiation to be successful, a large number of data points is necessary (about 500 or more), and the curves cannot be too noisy. Ideally, the curve should have reached a plateau; at the very least, it is necessary to collect data for a period = 3τ (Fig. 11.5), otherwise the result may be meaningless. 14. To obtain a meaningful fit, the data must be collected for a period of at least 2.5 times the longest τ i (Fig. 11.5). If the curves contain a small initial inflection or sigmoidicity (a lag period), a good fit can still be obtained if one of the amplitudes (α i ) is negative (see legend of Fig. 11.5). However, for curves with long lags, which occur with some peptides, such as ␦-lysin (6), this type of fit would require

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a series of exponentials with negative amplitudes, which quickly becomes a complicated task.

Acknowledgments This work was supported by National Institutes of Health grant No. GM072507. We thank Erin Kilelee for her help during the preparation of the manuscript. References 1. Vaz, W. L., Kaufmann, K., and Nicksch, A. (1977) Use of energy transfer to assay the association of proteins with lipid membranes. Anal. Biochem. 83, 385–393. 2. Gregory, S. M., Cavenaugh, A., Journigan, V., Pokorny, A., and Almeida, P. F. F. (2008) A Quantitative model for the all-or-none permeabilization of phospholipid vesicles by the antimicrobial peptide cecropin A. Biophys. J. 94, 1667–1680. 3. Hope, M. J., Bally, M. B., Webb, G., and Cullis, P. R. (1985) Production of large unilamellar vesicles by a rapid extrusion procedure. Characterization of size distribution, trapped volume and ability to maintain a membrane potential. Biochim. Biophys. Acta 812, 55–65. 4. Weinstein, J. N., Yoshikami, S., Henkart, P., Blumenthal, R., and Hagins, W. A. (1977) Liposome-cell interaction. Transfer and intracellular release of a trapped fluorescent marker. Science 195, 489–492. 5. Kayalar, C. and Düzgüneçs, N. (1986) Membrane action of colicin El. Detection by the release of carboxyfluorescein and calcein from liposomes. Biochim. Biophys. Acta 860, 51–56. 6. Pokorny, A., Birkbeck, T. H., and Almeida, P. F. F. (2002) Mechanism and kinetics of ␦-lysin interaction with phospholipid vesicles. Biochemistry 41, 11044–11056. 7. Pokorny, A. and Almeida, P. F. F. (2004) Kinetics of dye efflux and lipid flip-flop induced by ␦-lysin in phosphatidylcholine vesicles and the mechanism of graded release by amphipathic, ␣-helical peptides. Biochemistry 43, 8846–8857. 8. Yandek, L. E., Pokorny, A., Florén, A., Knoelke, K., Langel, U., and Almeida, P. F. F. (2007) Mechanism of the cellpenetrating peptide transportan 10 permeation of lipid bilayers. Biophys. J. 92, 2434–2444.

9. Gregory, S. M., Pokorny, A., and Almeida, P. F. F. (2009) Magainin 2 revisited: a test of the quantitative model for the allor-none permeabilization of phospholipid vesicles. Biophys. J. 96, 116–131. 10. Chen, R. F. and Knutson, J. R. (1988) Mechanism of fluorescence concentration quenching of carboxyfluorescein in liposomes: energy transfer to nonfluorescent dimers. Anal. Biochem. 172, 61–77. 11. Schwarz, G. and Robert, C. H. (1990) Pore formation kinetics in membranes, determined from the release of marker molecules out of liposomes or cells. Biophys. J. 58, 577–583. 12. Robert, C. H. and Schwarz, G. (1992) Kinetics of pore-mediated release of marker molecules from liposomes or cells. Biophys. Chem. 42, 291–296. 13. Rex, S. and Schwarz, G. (1998) Quantitative studies of the melittin-induced leakage mechanism of lipid vesicles. Biochemistry 37, 2336–2345. 14. Pokorny, A., Yandek, L. E., Elegbede, A. I., Hinderliter, A., and Almeida, P. F. F. (2006) Temperature and composition dependence of the interaction of ␦-lysin with ternary mixtures of sphingomyelin/cholesterol/POPC. Biophys. J. 91, 2184–2197. 15. Vaz, W. L. C. and Hallmann, D. (1983) Experimental evidence against the applicability of the Saffman-Delbrück model to the translational diffusion of lipids in phosphatidylcholine bilayer membranes. FEBS Lett. 152, 287–290. 16. Haugland, R. P. (2002) Handbook of Fluorescent Probes and Research Products (9th ed.). Eugene: Molecular Probes. 17. Kates, M. (1972) Techniques in lipidology. In Laboratory Techniques in Biochemistry and Molecular Biology. Work, T. S. and Work, E. (Eds.), Amsterdam: North-Holland Publishing Company.

Peptide Interactions with Model Membranes 18. Bartlett, G. R. (1959) Phosphorous assay in column chromatography. J. Biol. Chem. 234, 466–468. 19. Wimley, W. C. and White, S. H. (2000) Determining the membrane topology of peptides by fluorescence quenching. Biochemistry 39, 161–170.

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20. Yandek, L. E., Pokorny, A., and Almeida., P. F. F. (2008) Small changes in the primary structure of transportan 10 alter the thermodynamics and kinetics of its interaction with phospholipid vesicles. Biochemistry 47, 3051–3060.

Chapter 12 Comparing Bacterial Membrane Interactions of Antimicrobial Peptides and Their Mimics Nathaniel P. Chongsiriwatana and Annelise E. Barron Abstract Interactions with bacterial membranes are integral to the mechanisms of action of all antimicrobial peptides (AMPs), regardless of their final cellular targets. Here, we describe in detail two biophysical techniques that can be used to measure the membrane activities of AMPs and antimicrobial peptidomimetics: (1) a calcein leakage assay to investigate interactions between AMPs/peptidomimetics with large unilamellar vesicles and (2) a potential-sensitive dye-based depolarization assay to investigate interactions with the membranes of live bacteria. By comparing the membrane interactions of AMPs and their mimics, these techniques can provide insights into their extent of mimicry and their antimicrobial mechanisms. Key words: Calcein leakage, large unilamellar vesicles, membrane depolarization, membrane potential, diSC3–5.

1. Introduction Many antimicrobial peptidomimetics, such as ␤-peptides (1, 2), ␤-peptoids (3), ␣/␤-peptides (4), oligoureas (5), oligo (phenylene ethynylene)s (6), and peptoids (7–9), successfully emulate antimicrobial peptide (AMP) function within a nonnatural framework; that is, mimicry of AMP structure generally leads to mimicry of AMP function. However, because the mechanisms of action of AMPs themselves are poorly understood, it is difficult to discern whether antimicrobial peptidomimetics kill bacteria via the same mechanisms as the peptides that they emulate.


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Here, we discuss two techniques that can be used to establish, to some degree, the extent of mechanistic analogy between AMPs and their mimics. Since membrane interactions are integral to the mechanisms of all AMPs regardless of their final targets (10, 11), calcein leakage assays (12–17) and bacterial membrane potential measurements (18–26) can be used to probe peptidomimeticmembrane interactions and compare them to like interactions with AMPs. Fluorescence monitoring of leakage from lipid vesicles is a model system used to evaluate membrane permeabilization by AMPs. This relatively simple model isolates the membrane and eliminates the possibility of interactions with other cellular components, which could confound the interpretation of results. However, leakage results must be seen within a broader context, since such other interactions also may prove integral to the overall mechanism. Typically, large unilamellar vesicles (LUVs) are used for leakage studies, with a variety of dyes entrapped therein, such as calcein (12–17), carboxyfluorescein (27–29), FITC-labeled dextrans (16, 17), and dipicolinic acid, the latter of which forms a fluorescent complex with terbium(III) (27, 28). In a calcein leakage assay, the dye is entrapped inside LUVs at a high, self-quenching concentration of 70 mM. If the membrane is permeabilized, dye leaks out of the vesicles, becomes diluted by the extra-vesicular buffer, and begins to fluoresce. The amount of calcein dequenching is then quantified relative to a 100% leakage control (typically a detergent like Triton X-100). Rather than measuring the leakage of artificial fluorophores from model vesicles, membrane permeabilization can also be studied by monitoring the translocation of physiological species, like protons or other small ions, across membrane bilayers. As with leakage assays, this can be accomplished with fluorescence spectroscopy using fluorescent dyes that are sensitive to changes in transmembrane potential or intracellular pH (29), such as diSC3–5 (30), BCECF-AM (31), 9-aminoacridine (32), and oxonol VI (33). Bacteria typically have an inside-negative transmembrane potential that arises from the interplay between charge gradients and concentration gradients across the plasma membrane. This is made possible by the selective permeability of the plasma membrane to certain ions, particularly K+ , Na+ , and Cl– (34). A number of net-anionic proteins are concentrated in the cytoplasm, whose charge is balanced by positively charged counterions. Were the membrane impermeable to every species, no electrical potential would be generated, since both anions and counterions would be restricted to the cytoplasm, albeit against their concentration gradients. However, bacterial membranes contain a number of protein channels that each accommodate a specific ion, such as the potassium channel KcsA (35). Potassium

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can freely diffuse through this channel, and so a small number of K+ ions leak out of the cell down their concentration gradient. In contrast, anionic proteins are held in the cytoplasm, thereby creating a charge imbalance, and the cell is left with an inside-negative voltage across the plasma membrane. Note that many different ions are responsible for the overall membrane potential, although the contributions of potassium and sodium predominate. DiSC3–5 is perhaps the most commonly used potentialsensitive dye and is particularly useful because it can be employed in conjunction with live bacteria in addition to lipid vesicles (18–26). A cationic cyanine, diSC3–5, accumulates in the electronegative cell interiors, where its fluorescence is self-quenched. Membrane disruption by AMP-mimetic oligomers can cause a loss of the membrane’s selective ion permeability, leading to depolarization (dissipation of the membrane potential). As a result, the dye is released from the cell and its subsequent fluorescence can be quantified relative to the action of a molecule, such as melittin, an amphipathic, cationic peptide that is known to depolarize bacteria completely.

2. Materials 2.1. Calcein Leakage Assay

1. Self-quenching aqueous calcein solution: 70 mM calcein, 10 mM Tris–HCl, pH 7.4 (see Note 1).

2.1.1. Extrusion of Calcein-Filled LUVs

2. Extra-vesicular buffer: 10 mM Tris–HCl, 100 mM NaCl, pH 7.4 (36–39). 3. Lipids [cholesterol, palmitoyloleoylphosphatidylcholine (POPC), palmitoyloleoylphosphatidylethanolamine (PO PE), palmitoyloleoylphosphatidylglycerol (POPG), etc.] (Avanti Polar Lipids, Alabaster, AL, USA) are purchased as lyophilized powders, weighed out, and dissolved in chloroform to a final known stock concentration (typically around 10.0 mg/mL). Store at –20ºC for up to 2 weeks; stock solutions should be allowed to reach room temperature before using and should be clear and colorless. 4. LUV extruder (Avanti Polar Lipids) with accompanying short-needle Hamilton syringes, polycarbonate membrane filters with 0.1 ␮m pores (larger sizes are optional; see Note 2). 5. Liquid nitrogen. 6. Water bath at 35–40ºC.

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2.1.2. Separation of Calcein-Filled LUVs from Free Calcein

1. Sephadex G-50, medium grain, swollen by boiling in distilled, deionized water for approx. 1 h. Boiling the slurry accelerates swelling of the gel and degasses the water to prevent the appearance of air bubbles after packing the column. The amount of water in the gel suspension should be adjusted to approx. 75% settled gel. Store at room temperature. 2. Glass column with 1 cm inner diameter, ∼30 cm length, fritted glass bottom, and stopcock.

2.1.3. Phosphorus Assay to Determine Lipid Concentration of Calcein-Filled LUVs After Gel Filtration

1. Digestion acid: concentrated H2 SO4 plus 70% HClO4 (2:1). Store at room temperature; discard if not colorless. 2. Phosphate solutions for standards: 10 and 1 mM aqueous monobasic sodium phosphate (NaH2 PO4 ). Store at room temperature. 3. Aqueous solution of 0.5% (w/w) ammonium molybdate tetrahydrate [(NH4 )6 Mo7 O24 ·4H2 O] for developing the color reaction. Store at room temperature. 4. 1-Amino-2-naphthol-4-sulfonic acid (ANSA) reagent (commercially available from Fisher Scientific, Pittsburgh, PA, USA): mix 1 g/L ANSA, 37 g/L sodium sulfite (Na2 SO3 ), and 62 g/L sodium metabisulfite (NaHSO3 ) in water. Store at –20ºC for up to 2 months. 5. Glass test tubes. 6. Sand bath or test tube heating block.

2.1.4. Measuring Calcein Leakage

1. Rectangular quartz fluorescence cuvette, 1.5 mL volume. 2. Extra-vesicular buffer: 10 mM Tris–HCl, 100 mM NaCl, pH 7.4. 3. Aqueous stock peptidomimetics.

solutions

of

peptides

and/or

4. 100% leakage control: 10% (v/v) aqueous Triton X-100 detergent. 2.2. Membrane Depolarization Assay 2.2.1. Preparation of Bacterial Suspension

1. Gram-negative (i.e., Escherichia coli ATCC 35218) or Gram-positive (i.e., Bacillus subtilis ATCC 6633) bacteria, grown to mid-logarithmic phase in standard growth medium, such as Luria–Bertani (LB) broth or Mueller– Hinton broth (MHB), made according to manufacturer’s instructions. 2. Respiration buffer: 5 mM HEPES, 20 mM glucose, pH 7.4. Store in the dark, as HEPES can develop toxic by-products when exposed to light.


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3. Dye stock: 30 ␮M 3,3’-dipropylthiadicarbocyanine iodide (diSC3–5) in DMSO. Store in the dark at 4ºC and let thaw at room temperature before using. 4. 0.5 M aqueous EDTA, pH 8.0 (see Note 3). 2.2.2. Measuring Membrane Depolarization

1. Rectangular quartz fluorescence cuvette, 1.5 mL volume. 2. Aqueous stock peptidomimetics.

solutions

of

peptides

and/or

3. 100% depolarization control: aqueous melittin stock solution, at an accurately known concentration of ∼10.0 mg/mL.

3. Methods 3.1. Calcein Leakage Assay

1. In a glass vial, combine lipid stock solutions (in chloroform) in the desired molar ratio to a combined mass of 20–50 mg (see Note 4).

3.1.1. Extrusion of Calcein-Filled LUVs

2. Dry the lipid mixture to obtain a film on the side of the vial by rotating slowly under a stream of nitrogen. 3. Lyophilize the chloroform.

film

overnight

to

remove

residual

4. Add enough buffered calcein solution (see Section 2.1.1) to bring the lipids to a concentration of 10–30 mM. 5. Let the lipid film hydrate in a water bath at 35–40ºC for 1 h. 6. After hydration, vortex the lipid suspension until no traces of the lipid film remain on the sides of the vial. The suspension now contains multilamellar vesicles (MLVs). 7. Subject the MLV suspension to 5 freeze/thaw cycles (liquid N2 /35–40ºC water bath). 8. Assemble the extrusion device according to the manufacturer’s instructions, using two stacked polycarbonate filters with 100 nm pores, then load the MLV suspension into one of the syringes. 9. Pass the suspension through the 100 nm pores 15 times (40). The suspension will become considerably more translucent as the MLVs are extruded into large unilamellar vesicles (LUVs). For some lipid compositions, preliminary extrusion through a larger pore size may be necessary (see Note 2). After the final passage, the LUV suspension should be in the syringe opposite to the starting syringe.

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This ensures that as few MLVs as possible are present in the final suspension. 3.1.2. Separation of Calcein-Filled LUVs from Free Calcein

1. Prepare a gel filtration column by pouring the slurry of hydrated Sephadex G-50 into a 1 cm inner diameter glass column. Allow the gel to settle completely before proceeding. The final settled height of the gel inside the column should be 6–10 cm. 2. Open the column stopcock and let the water above the gel drain. Do not let the liquid level fall below the top of the gel, or air will be introduced into the column and it will not permit adequate separation. 3. Equilibrate the column by flowing at least two column heights of extra-vesicular buffer (see Section 2.1.1) through the column (see Note 5). 4. To prepare to add the LUV suspension, let the level of buffer above the column fall just to the top of the gel, but not below. 5. Using a long Pasteur pipette, transfer the LUV suspension to the top of the column. Open the stopcock until the liquid level once again falls just to the top of the gel. Moving quickly, carefully add at least two column heights of extra-vesicular buffer to the top of the column and open the stopcock. 6. Watch the effluent closely. The calcein-filled LUVs will elute before the free calcein and appear visibly turbid compared to the free calcein solution. 7. As soon as the turbid LUVs begin to elute, start collecting fractions (∼0.3–1 mL each). Recombine the fractions containing the most LUVs (i.e., turbidity) and with least free calcein (i.e., color without turbidity). The resulting purified LUV suspension should be light orange in color and somewhat iridescent. Store at 4ºC for up to 1 week, although the performance of the vesicles will degrade over time as the entrapped calcein slowly leaks out of the vesicles into the surrounding buffer (this can be detected by an increase in the fluorescence of the suspension).

3.1.3. Phosphorus Assay to Determine Lipid Concentration of Calcein-Filled LUVs After Gel Filtration

This assay was adapted from Bartlett (41). 1. To create phosphorus standards, carefully pipette 50 ␮L of 1 mM NaH2 PO4 and 10, 20, 30, and 40 ␮L of 10 mM NaH2 PO4 into separate test tubes. Leave one tube empty. These standards contain 0, 50, 100, 200, 300, and 400 nmol of phosphorus. 2. Estimate the phosphorus concentration of the LUV suspension, accounting for the fact that the lipids will have


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been diluted during gel filtration. Since there is 1 phosphorus atom per lipid molecule (except cholesterol), the molar phosphorus concentration is equal to the molar lipid concentration. Using the estimated phosphorus concentration, pipette enough LUV suspension into a test tube to yield ∼200 nmol phosphorus. Make triplicates of each unknown at two different volumes to ensure that one set of unknowns will fall on the standard curve. For example, if lipids were extruded at 20 mM, typically three unknown samples of 20 ␮L LUV suspension and three of 40 ␮L LUV suspension will yield data that fall on the standard curve. 3. Dry unknown and standard samples in a sand bath or heating block at 100ºC for 1 h. 4. To each sample, add three drops of concentrated sulfuric acid/perchloric acid mixture (digestion acid, see 2.1.3.). 5. To digest samples, heat in sand bath or heating block above 250ºC until the samples are clear and colorless (approx. 1–2 h). 6. To each sample, add 1.8 mL 0.5% (w/w) aqueous ammonium molybdate and mix (see 2.1.3.). 7. Add 20 ␮L of ANSA reagent (see 2.1.3.). 8. Let color develop for at least 30 min at room temperature. 9. In a spectrophotometer, read the absorbance of the samples at 660 nm. 10. Plot A660 versus nanomoles of P for the standards, fit a line, and use the resulting trend line to calculate the lipid concentration of the LUV suspension (typically ∼1–10 mM). If the LUVs contain cholesterol, be sure to account for the fact that cholesterol does not contain phosphorus when calculating the total lipid concentration of the suspension. 3.1.4. Measuring Calcein Leakage

1. Set the fluorometer to measure fluorescence intensity at λexcitation = 490 nm, λemission = 520 nm, and a bandwidth of 1 mm. 2. Pipette 1.5 mL extra-vesicular buffer (see Section 2.1.1) into a rectangular quartz fluorescence cuvette. 3. Begin recording the fluorescence. 4. Pipette enough of the LUV suspension into the cuvette to have a final concentration of 50 ␮M lipids and aspirate gently to mix. The signal increases sharply and quickly stabilizes, reflecting the background fluorescence of the LUV mixture; this value is taken as 0% leakage for this particular run.

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5. After the background fluorescence stabilizes, pipette the appropriate amount of aqueous peptide or peptidomimetic stock solution into the cuvette to achieve the desired final peptoid or peptide test concentration. Aspirate gently to mix. If leakage occurs, dilution of the calcein by the extravesicular buffer causes dequenching and the fluorescence increases. 6. After 5 min, add 5 ␮L of 10% (v/v) aqueous Triton X100 and mix to get the maximal fluorescence value (100% leakage) for this particular run. The percent dequenching (percent leakage) after 5 min is given by

%Dequenching =

(F − F0 ) × 100 (FT − F0 )

where F is the fluorescence 5 min after the addition of the peptide/peptidomimetic, F0 is the initial fluorescence (before peptide addition), and FT is the total fluorescence (after Triton X-100 addition). 7. Repeat Steps 2–6 for each desired concentration of peptide or peptidomimetic to generate a curve of % dequenching (leakage) after 5 min versus peptide/peptidomimetic concentration. 3.2. Membrane Depolarization Assay 3.2.1. Preparation of Bacterial Suspension

1. Grow bacteria at 37ºC in growth medium (i.e., LB broth or MHB) to the mid-logarithmic phase. 2. Centrifuge bacterial culture at 2500×g for 10 min at room temperature. 3. Draw off supernatant and discard. 4. Resuspend the bacterial pellet in respiration buffer (see Section 2.2.1). 5. Add enough bacterial suspension to 25–40 mL fresh respiration buffer to make a dilute suspension with an optical density OD590 0.05. 6. Divide the dilute suspension into 1.5 mL aliquots. Each aliquot should be dyed with diSC3–5 1 hour before measuring depolarization by adding DMSO dye stock to a final dye concentration of 0.2 ␮M (see Notes 6–8). 7. For E. coli and other Gram-negative bacteria, 0.5 M aqueous EDTA may be added to a final concentration of 0.1–0.2 mM to each aliquot immediately before addition of dye in order to facilitate penetration of the dye through the outer membrane into the bacteria (see Note 9).


3.2.2. Measuring Membrane Depolarization

179

1. Set the fluorimeter to measure fluorescence intensity at λemission = 670 nm, λexcitation = 622 nm, and a bandwidth of 1 mm. 2. One hour after adding dye to the suspension aliquot, transfer the aliquot to a 1.5 mL rectangular quartz fluorescence cuvette. 3. After recording the baseline fluorescence, pipette the appropriate amount of aqueous peptide/peptidomimetic stock solution into the cuvette to achieve the desired final test concentration. Aspirate gently to mix. If depolarization occurs, the change in membrane potential causes dequenching of the diSC3–5 and the fluorescence increases. 4. Five minutes after the addition of peptide/peptidomimetic, pipette aqueous melittin stock to a final concentration of 20 ␮M to obtain the maximal depolarization for this particular run. Percent depolarization is calculated analogously to that in calcein leakage experiments: %Depolarization =

(F − F0 ) × 100 (FM − F0 )

where F is the fluorescence 5 min after the addition of the peptide/peptidomimetic, F0 is the initial fluorescence (before peptide addition), and FM is the total fluorescence (after melittin addition). 5. Repeat Steps 2–4 for each desired concentration of peptide or peptidomimetic to generate a curve of % depolarization after 5 min versus peptide/peptidomimetic concentration.

4. Notes 1. Because each molecule of calcein can donate four protons in solution, calcein will quickly acidify a solution, preventing further dissolution of the compound. To make 25 mL of the buffered 70 mM calcein solution, bring 1.089 g calcein and 0.0303 g Tris–HCl up to 25 mL with deionized water; the calcein will remain undissolved. Add saturated aqueous NaOH dropwise until the EDTA dissolves, then bring the pH back down to 7.4 with concentrated HCl. 2. Some lipid compositions (i.e., POPC/cholesterol) will be much more difficult to extrude than others (i.e., POPE/POPG); that is, such compositions may require much more pressure to extrude, sometimes enough to rupture the polycarbonate membrane filters. For these

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compositions, it may help to extrude the lipids first through membranes with larger pores (i.e., 600 or 400 nm) then move to increasingly smaller pores and finishing with 100 nm. 3. Like calcein, EDTA will not dissolve at high concentrations until the pH is raised to 9–10. To make 50 mL of 0.5 M aqueous EDTA, bring 9.306 g EDTA up to 50 mL with deionized water. Add saturated aqueous NaOH dropwise until the EDTA dissolves, then bring the pH back down to 8.0 with concentrated HCl. 4. Two examples of model lipid compositions are POPC/cholesterol (2:1) for erythrocyte-mimetic vesicles (42) and POPE/POPG (7:3) for bacteria-mimetic vesicles (43). 5. If liquid flows through the column too slowly, remove some of the gel. 6. The dye incorporates slowly into the bacteria (over ∼30 min) and its fluorescence is quenched in the process. 7. Each aliquot of suspension must be dyed separately because the fluorescence response of diSC3–5 to depolarization varies with the amount of time it has been in contact with the bacteria. Thus, all aliquots of dyed bacterial suspension must be used the same amount of time after addition of dye to ensure consistency of response. 8. Some published diSC3–5 depolarization protocols involve the use of 100 mM KCl to equilibrate the inner and outer K+ concentrations prior to measurement of depolarization (18, 19, 23–25). However, in our hands, depolarization was observed in response to peptides/peptidomimetics using the above protocol, even without addition of KCl. Indeed, AMPs and their mimics are believed to cause a change in membrane potential via non-specific permeabilization of bacterial membranes; thus, depolarization should occur and be observable regardless of whether or not the inner and outer K+ concentrations have been equilibrated. 9. For each bacterium used, try running the assay first in the absence of EDTA to determine if an adequate fluorescence response can be observed without its addition.

Acknowledgments The authors would like to thank Professor Robert MacDonald, Dr. Joshua Rausch, Dr. Jiwon Seo, and Ms. Meera Rao for their assistance in the development of these protocols. This work was


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supported by a Department of Homeland Security Fellowship and NIH Grants 1 R01 HL67984 and 1 R01 AI072666. References 1. Seebach, D., Overhand, M., Kühnle, F. N. M., Martinoni, B., Oberer, L., Hommel, U., and Widmer, H. (1996) ␤-peptides: synthesis by Arndt-Eistert homologation with concomitant peptide coupling. Structure determination by NMR and CD spectroscopy and by X-ray crystallography. Helical secondary structure of a ␤-hexapeptide in solution and its stability towards pepsin. Helv. Chim. Acta 79, 913–941. 2. Porter, E. A., Weisblum, B., and Gellman, S. H. (2002) Mimicry of host-defense peptides by unnatural oligomers: antimicrobial beta-peptides. J. Am. Chem. Soc. 124, 7324–7330. 3. Hamper, B. C., Kolodziej, S. A., Scates, A. M., Smith, R. G., and Cortez, E. (1998) Solid phase synthesis of ␤peptoids: N-substituted ␤-aminopropionic acid oligomers. J. Org. Chem. 63, 708–718. 4. Epand, R. F., Schmitt, M. A., Gellman, S. H., Sen, A., Auger, M., Hughes, D. W., and Epand, R. M. (2005) Bacterial species selective toxicity of two isomeric alpha/betapeptides: role of membrane lipids. Mol. Membr. Biol. 22, 457–469. 5. Violette, A., Averlant-Petit, M. C., Semetey, V., Hemmerlin, C., Casimir, R., Graff, R., Marraud, M., Briand, J.-P., Rognan, D., and Guichard, G. (2005) N,N’-linked oligoureas as foldamers: chain length requirements for helix formation in protic solvent investigated by circular dichroism, NMR spectroscopy, and molecular dynamics. J. Am. Chem. Soc. 127, 2156–2164. 6. Arnt, L., and Tew, G. N. (2002) New poly(phenyleneethynylene)s with cationic, facially amphipathic structures. J. Am. Chem. Soc. 124, 7664–7665. 7. Patch, J. A., and Barron, A. E. (2003) Helical peptoid mimics of magainin-2 amide. J. Am. Chem. Soc. 125, 12092–12093. 8. Seurynck, S. L., Patch, J. A., and Barron, A. E. (2005) Simple, helical peptoid analogs of lung surfactant protein B. Chem. Biol. 12, 77–88. 9. Statz, A. R., Meagher, R. J., Barron, A. E., and Messersmith, P. B. (2005) New peptidomimetic polymers for antifouling surfaces. J. Am. Chem. Soc. 127, 7972–7973. 10. Brogden, K. A. (2005) Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria? Nat. Rev. Microbiol. 3, 238–250.

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Chapter 13 Dynamic Transitions of Membrane-Active Peptides Stephan L. Grage, Sergii Afonin, and Anne S. Ulrich Abstract Membrane-active peptides or protein segments play an important role in many biological processes at the cellular interface to the environment. They are involved, e.g., in cellular fusion or host defense, where they can cause not only merging but also the destabilization of cell membranes. Many factors determine how these typically amphipathic peptides interact with the lipid bilayer. For example, the peptide orientation in the membrane determines which parts of the peptide are exposed to the hydrophobic bilayer interior or to the polar lipid/water interface. As another example, oligomerization is required for many activities such as pore formation. Peptides have been often classified according to a single characteristic mode of interaction with the bilayer, but over the years a more versatile picture has emerged. It appears that any single peptide can adopt several different alignments and/or oligomeric states in response to changes in the environment. For instance, many antimicrobial peptides adopt a surface-parallel alignment at low concentration, but they tilt obliquely into or even fully insert transmembrane into the bilayer above a critical peptide-to-lipid ratio, often in the form of oligomeric pores. Similar changes in peptide orientation or oligomeric state have been observed as a function of, e.g., temperature, lipid composition, pH, or induced by a synergistic partner peptide. Such transitions between peptide states can be regarded as the result of a re-adjustment in the balance between peptide–peptide and peptide–lipid interactions, as the environment conditions are changed. Though often studied in model membrane systems, such rich variety of peptide states is even more likely to occur in native biomembranes with their diverse compositions and physicochemical properties. The ability to undergo transitions between different states thus plays a fundamental role for the biological activities of membrane-active peptides. Key words: Antimicrobial peptides, biological membranes, peptide structure, peptide orientation tilt, re-alignment, barrel-stave pore, toroidal wormhole pore, solid-state nuclear magnetic resonance, oriented circular dichroism, synergy

1. Introduction Biomembranes create a barrier between cells and their environment, providing control of and protection against any physical and chemical imbalance. They present a natural target for many A. Giuliani, A.C. Rinaldi (eds.), Antimicrobial Peptides, Methods in Molecular Biology 618, DOI 10.1007/978-1-60761-594-1 13, © Springer Science+Business Media, LLC 2010

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kinds of membrane-active peptides, which can destabilize this protective shield and/or translocate into the cytosol. These short peptides typically possess a pronounced amphipathicity which facilitates their integration into the lipid bilayer, and they do not appear to require any receptor proteins for recognition. Several different classes of membrane-active peptides are distinguished mainly on the basis of their predominant biological function, and an intriguing question concerns the selectivity of their interaction with the specific lipid composition of the target membrane. The so-called antimicrobial or host defense peptides are particularly active against bacteria, leading to the death of the intruding microorganism. Antiviral and antifungal peptides may also be categorized as self-defense peptides, yet they are supposed to interact with non-prokaryotic membranes. Quite spectacular are anticancer peptides and some toxins that are lethal against specific mammalian (human) cells. Another related class of fusogenic peptides is capable of promoting fusion between lipid bilayers in vitro and in vivo. More recently, cell penetration has been linked to certain peptide sequences, coined cell-penetrating peptides or protein-transducing domains. Today, the boundaries between these different categories of membrane-active peptides are getting increasingly diffuse, as many peptides have been demonstrated to exhibit several different activities at the same time (1–4). It is obvious that many of the diverse biological activities are based on similar physicochemical principles of peptide–lipid interactions. To get better insight into the underlying mechanisms of membrane recognition, perturbation, and bilayer translocation, numerous peptides have been extensively studied (5–8). Prominent examples are the ␣-helical antimicrobial peptides magainin 2 and PGLa from frog skin, the bee venom peptide melittin, and the fungal peptide alamethicin. All of these have been found to permeabilize membranes, albeit in different ways (see Fig. 13.1). In the “carpet model,” the peptides are thought to disturb the integrity of the membrane by binding to its surface at a high concentration that changes the mechanical properties of the bilayer and causes a spontaneous local collapse. A “detergent-like” mechanism has also been proposed, wherein the amphiphilic peptides dissolve the lipid bilayer, yielding micellar or bicellar membrane patches. Finally, peptides can also increase permeability of the membrane by direct pore formation. Such pores can be lined by the peptide as in the “barrel-stave” model, or the peptides can stabilize a pore that is intrinsically formed by lipids according to the “wormhole” model. The different models of peptide–lipid interactions have offered explanations for the activities of various peptides considered in the individual studies. An underlying assumption has often been that there should be a single mode of action in each case, and just one dominant mode of peptide–lipid interactions

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Fig. 13.1. Different modes of membrane interaction suggested for membrane-active peptides: (a) binding to the bilayer or water interface; (b) “carpet”-like interaction; (c) detergent-like action; (d) disintegration of the bilayer producing bicelle-like discs; (e) transient or long-lived “barrel-stave”; (f) “toroidal” or “wormhole” pores; (g) insertion into a transmembrane alignment; (h) formation of a “slit”; (i) diffusion across the membrane; (j) modulation of the membrane curvature, induction of non-bilayer lipid phases and/or translocation via an inverted micelle.

intrinsic to each system. The mechanism of action has thus been attributed to the particular state the peptide had been found to adopt. For example, the surface alignment of an antimicrobial peptide has been taken to reflect a carpet-like interaction with the membrane, whereas an upright transmembrane alignment implied a pore mechanism, and motionally averaged molecules would have to be part of a micelle. However, such concept of characteristic states representing any one type of mechanism might be misleading. Accumulating evidence suggests that most peptides can assume several different states, and the transitions between these states need to be considered to explain the activity of each particular peptide system. Antimicrobial peptides, e.g., have been found to change their tilt angle with respect to the membrane as a function of temperature (9, 10), as a function of the peptide-tolipid ratio (11–15), as a function of lipid composition and bilayer hydration, etc. (16). More remarkably even, fusogenic peptides have been shown to change their membrane-bound conformation and mode of interaction in response to the peptide-to-lipid ratio (17–21) and as a function of pH (22–24). Also the fusion activity itself can be modulated by pH and ionic strength (25), and ionic strength influences the oligomerization and conformation of melittin in solution and modulates its bactericidal activities (26). Some cell-penetrating peptides have been found to aggregate above certain threshold concentrations, which leads to a modulation in the ratio of free peptide vs. aggregated one and influences the effective amount of transduction-competent species (27).

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In this review we highlight the diverse behavior of membraneactive peptides undergoing dynamic transitions, in which they change between different states as a response to changes in the bilayer and/or their environment. In the first section several relevant parameters characterizing the different states of membranebound peptides will be presented. The second section addresses the conditions leading to structural transitions between different peptide states in model membranes. Finally, we discuss these transitions in the context of peptide–peptide and peptide–lipid interactions.

2. MembraneActive Peptides in Different States

2.1. Peptide Conformation

At first the question arises as to how the different states of a peptide in the membrane can be defined and characterized. One way is to use experimentally accessible parameters that reflect the mode of membrane activity of the peptide. Membrane interactions of peptides have been studied with an enormous range of different techniques. In the following we give a brief overview of the different parameters typically addressed. The physicochemical properties of peptides and many aspects of peptide–lipid or peptide–peptide interactions are determined by the three-dimensional structure of the peptide. For instance, a peptide is only able to display its (secondary) amphipathicity when in the right fold. Yet there seems to be no particular structure required for membrane activity. For example, antimicrobial effects can be exerted by ␣-helical peptides, such as magainin or melittin, but also by ␤-helical, ␤-stranded, or ␤-turn containing peptides, such as gramicidin A, gramicidin S, or protegrin 1, respectively, to name just a few (28). Cell-penetration activity may even be mediated by merely the presence of appropriately spaced guanidinium moieties, irrespective of the peptide (or peptidomimetic) backbone conformation (29). For one of the most well-studied fusogenic peptides, FP23 from HIV gp41, the question whether the structure of its active form is either ␣-helical, ␤-stranded, or something else is still under debate (30–33). Linear peptides such as antimicrobial sequences with typically 10–30 amino acids tend to be highly flexible in aqueous solution, as they often lack stabilizing intramolecular interactions. The structure thus depends strongly on the dielectric properties of the environment, such as a solvent or a lipid bilayer. Therefore, it is not surprising that antimicrobial peptides often adopt their functionally relevant conformation only when they are embedded in the membrane. Hence, a defined secondary structure often

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indicates binding of the peptide and can thus reflect the adoption of a membrane-active state. As the environment of the peptide is a crucial determinant of its conformation, reconstitution in a lipid bilayer or a membranemimicking environment is a prerequisite for obtaining a functionally relevant structure, which raises the question as to the relevance of X-ray crystallization results. Circular dichroism is well compatible with studies of membrane-active peptides and represents the most useful routine tool to evaluate qualitative secondary structures. For a full three-dimensional structure analysis in a lipid bilayer or a membrane-mimicking environment, NMR spectroscopy plays an essential role. For soluble proteins of moderate size, solution state NMR represents an established route to obtain structures at atomic resolution. This technique is applicable to membrane-associated peptides, provided a suitable membrane mimic can be found. Often organic solvents such as trifluoroethanol (TFE), ethanol, methanol, chloroform, acetonitrile, hexafluoroisopropanol, hexafluoroacetone, or DMSO, as well as their mixtures with water are used to provide a simple model of the hydrophobic membrane environment. However, in particular the use of TFE with ␣-helical peptides can be problematic, as this solvent enforces the formation of intramolecular hydrogen bonds; hence any observed helix or turn should be interpreted as a propensity for such conformation that is intrinsic to the peptide. DMSO as a solvent, on the other hand, is rather prone to disrupt secondary structures of peptides (since S=O is a stronger hydrogen bond acceptor than C=O). Hence it is most useful to study conformations that are stabilized by very strong intramolecular hydrogen bonds, e.g., in cyclic peptides. Even for such stable folds as that of the cyclic gramicidin S (two to four hydrogen bonds predicted), a slight but significant solvent dependence of the conformation has been observed (34–36). Gramicidin A, representing the first antimicrobial peptide whose three-dimensional membrane-bound structure has been solved, was studied at first using solution NMR, where a severe conformational heterogeneity depending on the membrane-mimetic solvent was observed (37–39). The conformation of gramicidin A dissolved in DMSO, in particular, turned out to be fundamentally different from its structure in flat bilayer membranes, as determined by solid-state NMR (see below). Instead of a head-to-head dimer of single-stranded right-handed ␤-helices, an intertwined left-handed double-helical structure was found, indicating that the environment has a severe impact on the fold and self-assembly. Instead of organic solvents, detergent micelles or isotropic bicelles provide an environment significantly closer to a lipid bilayer, while still allowing for the motional averaging necessary for solution state NMR. Numerous structures of membraneactive peptides have been determined this way (40–42). Though

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mimicking the hydrophobic interior of the membrane as well as the polar/apolar interface, micelles are not able to represent correctly the curvature of a membrane, possibly leading to deformed conformations for surfacially bound peptides (43, 44). To avoid such artifacts, isotropic bicelles, composed of a mixture of a detergent-like short-chain lipid and a long-chain lipid, have been used as an improved substitute (45). Ultimately, one aims at obtaining the peptide structure in a planar lipid bilayer (41, 46). However, the molecular weight of extended membrane systems exceeds by far the limit imposed by the need for fast isotropic tumbling, which is the basis of the high resolution achieved in solution state NMR (47). As an alternative, solid-state NMR has been employed in a number of cases to successfully obtain backbone structures of membrane-active peptides at atomic resolution. The “static” NMR signals of membranebound peptides exhibit a pronounced orientation dependence, which gives rise to characteristic line broadening but as a consequence leads to deleterious signal overlap. Two different strategies have been pursued to cope with this strong anisotropy of the NMR interactions (48, 49). Using magic angle spinning, reasonably rapid isotropic motion can be artificially introduced, and high resolution is achieved on the same grounds as in solution state NMR. As an alternative, and at least equally successfully, strategies have been developed to exploit rather than suppress the orientation dependence in uniaxially aligned membrane samples. The first solid-state NMR peptide structure, that of gramicidin A, has been acquired using this approach (50). The ␤-helix backbone structure and the tryptophan side chain conformations for this peptide have been assembled from orientation-dependent NMR signals of selective 15 N-, 13 C-, and 2 H-labels. 2.2. Alignment of Peptides in the Membrane

What defines the mode of membrane activity is often not only the three-dimensional structure as such, but also how the molecule is positioned with respect to the lipid bilayer. While the backbone conformation defines the amphipathic nature of the peptide, it is the molecular alignment in the membrane which determines whether the different faces of the folded molecule are exposed to the hydrophobic interior of the bilayer, to the apolar/polar interface, or to the aqueous subphase. The actual interaction of the peptide with the lipids and/or with other peptides therefore depends critically on its orientation with respect to the bilayer. As the interactions with the membrane are the underlying cause for membrane activity, the peptide alignment within the membrane is also indicative of the mechanistic mode of action. For many peptides, where amphipathicity divides the molecule into a hydrophilic and hydrophobic face (typically the apolar/polar dividing line may run along the long molecular axis in amphipathic ␣-helices and ␤-strands or along the backbone ring in

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“sided” cyclic peptides) it is the hydrophobic moment vector that characterizes the alignment (51, 52). For the most thoroughly studied cases of amphipathic ␣-helices, the hydrophobic moment has been found to orient either (roughly) parallel, to be tilted, or to be aligned nearly perpendicular to the membrane normal. Hence the alignment of the entire helix, seen as a conformationally rigid body, can be classified in terms of three distinct states. In the surface-aligned or “S”-state, the polar side of the peptide faces the aqueous phase, while the hydrophobic side points toward the core of the bilayer. In the tilted or “T”-state, the peptide is obliquely immersed in the bilayer with a slanted orientation. Finally, in the inserted or “I”-state, the peptide helix is fully inserted with its apolar/polar dividing line perpendicular to the membrane surface; hence both faces of the amphipathic peptide are positioned within the bilayer slab. Depending on its orientational state, different faces of the peptide are exposed to the interior of the bilayer or the aqueous subphase. In the S-state the peptide adapts optimally to the apolar/polar interface of the bilayer. As this state represents the natural alignment of any amphipathic membrane-bound peptide, it is the expected and indeed most frequently encountered alignment. This state allows extensive interactions of the peptide with the interface region of the membrane. Such mode of binding may lead to a destabilization of the bilayer if its physicochemical properties such as spontaneous curvature, molecular packing of certain lipids, or lateral stress profile are changed. This way, antimicrobial peptides can increase the membrane permeability in accordance with the “carpet model” (Fig. 13.1), and fusogenic peptides can promote curvature-driven stages of the bilayer fusion event. In the I-state, on the other hand, the polar face of the amphiphatic peptide is immersed in the hydrophobic interior of the membrane. A single molecule would not be stable in this alignment. However, by interacting with other peptides to form an oligomeric pore, with the hydrophilic face pointing inside, a disadvantageous exposure of the polar face to the hydrophobic lipid chains can be avoided. Antimicrobial peptides assume this orientational state when acting via the “barrel-stave” or “wormhole” mechanism. Likewise, amphiphilic ␣-helical cell-penetrating peptides have to adopt an inserted state at least in a transient fashion to be able to cross the membrane. Knowledge of the peptide orientation in the lipid bilayer thus gives crucial clues about its mode of membrane activity. The molecular alignment can be specified by two angles, the tilt angle τ and the azimuthal rotation ρ (see Fig. 13.2). It has been recently demonstrated that a distribution of tilt and rotation angles is present rather than a single alignment. It thus depends on the timescale of the experimental method, whether an averaged effective orientation or the distribution is accessible.

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Fig. 13.2. A number of orientational constraints (i.e., a set of local angles θ) have to be measured by solid-state NMR to calculate the peptide conformation (here: helical), its alignment (described by the tilt angle τ and the azimuthal rotation ρ), and its dynamic behavior in the lipid membrane.

Experimentally, the peptide orientation can be obtained either indirectly from the penetration depth of a set of probes introduced into the peptide or directly by using orientationdependent spectroscopic techniques. Depth measurements have been used in several recent fluorescence studies to address the inclination of a peptide (53–55). Exploiting the quenching of NMR probes by paramagnetic ions in the aqueous or membrane phase, it has also been possible to determine peptide orientation by solid-state NMR (56–58). To measure the alignment state directly, the anisotropic parameters accessible by many spectroscopic techniques can be exploited. Most of these rely on a uniform orientation of the studied peptide in a macroscopically aligned sample. Membranes can be aligned mechanically on glass plates or on other (inert polymeric) solid supports. Alternatively, bicelles formed by a mixture of a short-chain and a long-chain lipid provide a way to orient bilayers magnetically for anisotropic solid-state NMR studies. Optical techniques such as infrared spectroscopy (IR) or circular/linear dichroism on peptides in oriented bilayers provide a complementary way to qualitatively assess the peptide orientation. Particularly for α-helical antimicrobial peptides, oriented circular dichroism (OCD) has been a useful tool in determining their alignment state. The absorption of the CD band around 208 nm depends on the alignment between the electrical field component and the transition dipole moments associated with the peptide bond. An intense OCD signal is obtained if the α-helix is aligned perpendicular to the incident light, whereas the band practically disappears when the peptide long axis lies in the direction of the light propagator.

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While the theoretical complexity of OCD or polarized attenuated total reflection infrared spectroscopy (ATR-IR) limits the orientational analysis to rather qualitative conclusions, solid-state NMR with its simple and direct orientation dependencies can provide precise angular information even in atomic detail. To this aim, the anisotropic chemical shift or dipolar couplings of a set of isotope labels in the peptide are measured, and they are combined to yield the τ and ρ angles of the peptide. Several labeling schemes and associated experimental approaches have been applied. The backbone orientation of a given peptide can be directly addressed using 15 N or 13 C. In particular for uniformly 15 N-labeled α-helical peptides, the correlation of 15 N chemical shift anisotropy and 15 N–1 H dipolar coupling in the PISEMA or related experiments has been very successful. The α-helical pattern of the peptide is mapped directly onto a regular wheel-like pattern in the two-dimensional NMR spectrum, whose location in the spectrum yields the value of τ . The position of a single, selectively 15 N-labeled residue along the rim of the wheel, on the other hand, can reveal the azimuthal angle ρ of the peptide helix. Side chain labels, too, can be used to determine the peptide alignment, provided that the NMR label on the side chain is rigidly linked to the backbone. Using, for example, 2 H3 -alanine in the GALA approach, a number of peptide tilts have been determined (59, 60). More recently, some highly sensitive 19 F labels have also been employed in alignment studies of membrane-active peptides. Special amino acids were designed to provide a direct connection of the 19 F label with the peptide backbone, without altering their biological activity in most cases (61–65). The exquisite sensitivity has allowed systematic screening work to study the influence of various conditions on the peptide alignment behavior, rendering solid-state 19 F NMR a highly important tool for the discovery of transitions between peptide states.

3. Transitions Between Peptide States

Membrane-active peptides were originally thought to be associated with a specific biological function, as the result of the particular physicochemical properties of the peptide. However, numerous examples in which a peptide has been found to adjust to changes in the environment have become apparent over recent years. Hence it is clear that the behavior of peptides is not only governed by their intrinsic physical properties, but also strongly influenced by their interactions with the target membrane. As outlined in the first section, the mode of interaction of a peptide with membrane lipid bilayer is reflected in several

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observable parameters, such as the conformation, the molecular alignment in the membrane, or the oligomeric state. Many different states have been described, such as the S-state, T-state, I-state, monomeric, dimeric, oligomeric, barrel-stave, toroidal wormhole. Notable, a single peptide is likely to be able to adopt several of these states, which are not static but can interchange depending on various conditions. In the following we describe some of the most relevant changes in the environmental parameters that have been found to lead to transitions between states. 3.1. Peptide-to-Lipid Ratio

Perhaps the strongest influence on the state of a peptide is exerted by the peptide-to-lipid ratio (P/L), i.e., the peptide concentration in the membrane. Already in the 1990s, Huang et al. have suggested the presence of a critical concentration, separating two states with different alignments in the membrane (13). Many amphipathic α-helical peptides have been found since to change from a surface-bound S-state at low concentration to a tilted or inserted state at high concentration. For example, the antimicrobial PGLa adopts an angle of τ ∼ 98◦ (between the helix axis and the membrane normal), i.e., a helix alignment nearly parallel to the bilayer surface, below a threshold of approximately P/L = 1/50 to 1/100 (in DMPC) (11, 15, 16). Above this concentration, the tilt angle changes to τ ∼ 126◦ , and the peptide adopts an oblique T-state orientation (see Fig. 13.3). A similar behavior was found for other peptides with the same architecture, for example, MSI-103 and MAP. At low concentration, amphipathic α-helical peptides thus bind to the membrane adopting their alignment to the apolar/polar interface. If the peptide concentration exceeds a critical threshold, neighboring peptides will play a role in determining the favorable orientation. At high concentration the peptides then interact not only with the lipid bilayer alone, but also among themselves. A plausible model suggests that they may form

Fig. 13.3. Solid-state 19 F- and 2 H-NMR revealed the binding, folding, and dimerization of the antimicrobial peptide PGLa, and this was also observed for the related analogues MSI-103 and MAP (11, 12, 15, 16).

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dimers, as this would explain the stability of the otherwise less favorable tilted alignment of the amphiphile (11, 16). While increasing concentration of α-helical antimicrobial peptides leads to a transition from an S-state to a T-state, a complete I-state insertion was observed for cyclic ␤-sheet/␤-turn peptides such as gramicidin S and protegrin B (66, 67). For gramicidin S an insertion in an upright position in the membrane was observed for a peptide-to-lipid ratio above approximately 1/80 (in DMPC). Interestingly, this transition into the I-state was also found to be promoted at temperatures near the lipid phase transition, thus indicating a more complex dependence on different environmental conditions. To account for the immersion of the hydrophilic face of gramicidin S into the hydrophobic interior of the membrane in the I-state, self-assembly as a ␤-barrel pore was suggested as a stable H-bonded structure (66, 68) (see Fig. 13.4). A similar equilibrium between a monomeric S-state at low concentration and an insertion to form an oligomeric pore at high concentration was found for alamethicin (14). However, this transition exhibits also a rather different dependence on the lipid phase state (see below).

Fig. 13.4. Formation of a ␤-barrel pore by gramicidin S, a cyclic amphiphilic bacterial peptide.

Very large peptide assemblies in membranes have been visualized by atomic force microscopy (AFM), revealing extended striated domains over several micrometers for gramicidin A or the model peptide WALP reconstituted in solid-supported bilayers (69, 70, 82–84). Though arguably the solid support may influence the physical properties of the bilayer, peptide–peptide, and peptide–lipid interactions have comparable strengths, allowing for a broad range of oligomer sizes and supermolecular architectures in such peptide/lipid systems. Another type of aggregates frequently encountered with many peptides are fibrillar self-assemblies. Many diseases such as Alzheimer are connected to proteins or peptides assuming a pathogenic, supramolecular form, which often possesses a cross-␤-sheet secondary structure. Some of these proteins are themselves postulated to have a membrane-related activity. For

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example, the Alzheimer A␤ peptide is speculated to form ion channels (71, 72), for which a crowding model has been recently suggested (73). A similar behavior has been suggested for further peptides related to neurodegenerative diseases, such as ␣synuclein, and might be a more general phenomenon (74, 75). Following binding to the membrane and bilayer-induced conformational changes, an increase in peptide concentration here leads to the formation of fibrillar aggregates at the bilayer surface. Quite common are such observations where typical ␣-helical peptides were unexpectedly found to form amyloid fibrils under specific conditions. For example, the fusogenic protein segment B18 from the sea urchin fertilization protein bindin assembles as fibrils (17, 18, 20), and recently also the model amphipathic peptide MAP was encountered in a fibrillar form (76, 77). Only when aggregation is suppressed in MAP by inclusion of a rigid D -amino acid does it exhibit the typical concentration-dependent transition from a monomeric S- to a potentially dimeric T-state, similar to other peptides with the same architecture such as PGLa or MSI-103. It appears that the aggregation state plays a functionally relevant role in the use of MAP and other sequences as cell-penetration peptides (27). 3.2. Temperature Dependence

Concentration was long believed to be the dominant factor determining the state of membrane-active peptides. However, already in the early studies of alamethicin, Vogel, Huang and coworkers found a change in molecular alignment upon varying the temperature, which was recently confirmed by solid-state NMR and EPR (10, 14, 78, 79). At temperatures below the gel/liquid crystalline phase transition of the lipid bilayer, alamethicin was found in the S-state, whereas insertion of this rather hydrophobic sequence occurred at higher temperatures in the fluid phase. More recently, a different type of temperature-dependent realignment was encountered for the cyclic gramicidin S and for the α-helical amphipathic peptide PGLa (9, 66). As discussed above, gramicidin S adopts either a monomeric S-state or an inserted oligomeric state in the bilayer, the latter being favored at high peptide concentration. The transition into the I-state, however, was also found to depend on temperature, as it was only observed at temperatures near the gel/lipid phase transition of the bilayer. Furthermore, the temperature range over which the I-state is observed gets significantly wider with increasing peptide concentration. As the lipid phase transition also broadens with higher peptide concentration, the appearance of the I-state of gramicidin S thus seems to be connected to the lipid phase transition (and to the lipid chain length, see below). In the case of PGLa, a multi-stage re-alignment has been comprehensively analyzed by 2 H and 19 F NMR. A concentration-dependent transition from Sto T-state had been described and attributed to the formation of

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a putative homodimers at high concentration. Complete insertion into an I-state, however, could not be achieved by increasing the PGLa concentration further. Only by adding magainin 2, its synergistic partner peptide, could an I-state be achieved under ambient conditions (see below) (16, 80). However, as in the case of gramicidin S, also the temperature was found to be able to trigger the transitions between the S, T, and even the I-state (9) (see Fig. 13.5). Thus far only observed in the presence of magainin 2, upon lowering the temperature below the lipid phase transition PGLa was found to fully insert on its own in an I-state alignment. While this transition is related to the lipid phase state (acyl chain melting of DMPC at ∼24◦ C), a second temperaturedependent transition was observed at higher temperatures. Above about 45◦ C, PGLa no longer retains its T-state alignment at high concentration, but instead reverts to the monomeric S-state. This transition is not related to the lipid phase state, but might be attributed to a disintegration of the PGLa dimer.

Fig. 13.5. Temperature-dependent re-alignment of PGLa from S-state to T-state in fluid lipid bilayers, and its insertion as an oligomeric transmembrane pore in the gel phase.

Most temperature-dependent transitions of peptide states seem to be related to the melting transition of the lipid chains. Here the change in temperature leads to a different lipid environment, with significantly different physical properties. Many peptide transitions thus can be regarded as an adaptation to the respective membrane in the gel or fluid phase. As will be outlined below, a lipid bilayer in its different states possesses different thicknesses and molecular dynamics, leading to different lipid–lipid and lipid–peptide interactions depending on the bilayer phase state. Hence the balance of the interactions between the different molecules can be shifted, leading to changes in the oligomeric state or the insertion of the peptide upon going from one lipid phase to another. Some peptide states, however, are not associated with either the gel or the fluid phase of the membrane, but they exist only in the vicinity of the lipid phase transition temperature itself (as in the case of gramicidin S). These states

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appear to be related to local defects in the bilayer or to fluctuations between solid–fluid phase boundaries occurring at the lipid phase transition. Yet the PGLa example demonstrates that there also exist peptidic transitions disconnected from the lipid phase behavior, which are governed solely by peptide–peptide interactions. 3.3. Lipid Composition

Besides peptide–peptide interactions, peptide–lipid interactions are the determinants for the peptide behavior in the membrane environment. Both the lipid phase and the intrinsic properties of the lipids will exert an important influence on the peptide state. Such physicochemical aspects concern the hydrophobic thickness, the degree of chain saturation, headgroup type and charge, and the spontaneous curvature of the lipid bilayer. In biological membranes with their very diverse and complex lipid composition, particular properties can lead to distinctly different peptide activity. For example, cationic antimicrobial peptides are known to target the plasma membrane of the invading bacteria, but leave the host cell membranes intact. This selectivity is attributed to the fact that bacterial membranes tend to be negatively charged, whereas the plasma membrane of eukaryotic cells contains mainly zwitterionic lipids in its outer leaflet as well as a high amount of cholesterol. The membrane thickness is one of the parameters discussed intensively in the literature as determining the behavior of membrane-bound peptides. In particular, the concept of hydrophobic mismatch suggests that (predominantly hydrophobic) peptides tend to adapt their hydrophobic region to the thickness of the hydrophobic region of the bilayer. This concept was explored using the model peptide WALP and analogues thereof (81). Different possibilities were discussed controversially, namely that the peptide could adapt to a thinner membrane by assuming a tilted orientation, or that instead the annular lipids could adjust to the peptide by stretching their chains and changing the local bilayer curvature. Evidence for both scenarios has been found. For example, AFM studies of WALP and gramicidin A suggest an adaptation of the lipids to the peptide (69, 70, 82–84). On the other hand, tilt angle measurements using solid-state NMR can be interpreted as an adaptation of the peptide orientation to match the bilayer thickness, provided that mobility is considered in the data analysis (85, 86). While hydrophobic mismatch in the case of the WALP leads at most to a change in tilt angle, in the case of alamethicin the above-mentioned studies (78, 79) suggest that this peptide can no longer remain inserted in a membrane of inappropriate thickness and gets expelled (see Fig. 13.6). Besides the alignment in the membrane, also the mobility of a peptide can be influenced by the membrane thickness, as, for example, observed for (LA)n model peptides in a solid-state NMR study by Sharpe et al. (87). Here, peptide–peptide interactions were

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Fig. 13.6. In fluid membranes alamethicin forms a transmembrane barrel-stave type of pore, but it gets expelled from the bilayer at temperatures below the lipid chain melting transition, presumably due to hydrophobic mismatch.

modulated by the hydrophobic mismatch, and as a consequence, a different degree of mobility was observed and interpreted in terms of different oligomeric states. Despite their small dimensions, which are usually not sufficient to span the lipid bilayer, even cyclic ␤-sheet peptides have been found to exhibit a dependence on the bilayer thickness. For example, retrocyclin-2 assumes a tilted or surface alignment, depending on whether it is reconstituted in DLPC or POPC bilayers, respectively (88). As both lipids are in the fluid phase, the change in peptide orientation is clearly related to an adaptation to the different thickness of these bilayers. Also gramicidin S was found to exhibit a dependence on the bilayer thickness (89). As discussed already above, the usually surfacially aligned peptide inserts into the membrane close to the phase transition temperature. The temperature range for the I-state not only increases with increasing peptide concentration, but also changes with bilayer thickness. In membranes with increasing thickness, from DLPC to DPPC, the inserted state was found over a decreasing temperature range. Similar to alamethicin, these cyclic ␤-sheet peptides were thus also found to insert into the thinner membrane, whereas the mismatch in the thicker bilayer rendered insertion less favorable. While in most cases the lipid chains are responsible for the alignment or oligomeric state of the peptide, the lipid headgroups play an important role in the initial interaction with membraneactive peptides. In particular, the binding of peptides to the membrane is often mediated through electrostatic interactions, and the presence of charged residues influences this initial step of membrane activity. As many antimicrobial peptides are positively charged, negatively charged lipids have thus often found to enable or enhance peptide binding. For example, in aqueous solution PGLa has virtually no affinity to zwitterionic vesicles, but is stimulated in the presence of anionic lipids (16).

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3.4. Dependence on pH and Hydration

The amphipathic nature of membrane-active peptides is one of the main determinants of their behavior in the bilayer environment. As seen above, peptides align in membranes such as to match their hydrophobic faces with the bilayer interior, and the hydrophilic faces with the polar regions of the environment. Introducing a charged residue into a peptide can thus lead to a dramatic shift of this balance and lead to a transition from one state to another. In a number of examples, a pH change has been able to trigger such change of the total peptide charge. The fusion peptide of influenza hemagglutinin, for example, has been found to adopt a boomerang-like conformation with a different kink angle at acidic or neutral pH, allowing a deeper insertion at acidic pH and promoting fusion (90). Using histidine-containing LAHn model peptides, it has also been demonstrated that pH can be used to alter their orientation in the bilayer, by switching a hydrophobic helix into an amphipathic one upon histidine protonation (91). Hydration has been one of the first parameters found to influence the alignment state of antimicrobial peptides. In studies of alamethicin or melittin in oriented bilayer stacks using OCD, a re-alignment of these helices was observed upon varying the level of sample hydration (92–94). Here, dehydration was found to lower the critical peptide-to-lipid ratio, at which peptide insertion into the bilayer takes place. A fully hydrated interface region of the bilayer thus seems to be a prerequisite for a surface orientation, embedding the peptide according to its amphipathic nature into the polar/apolar interface region. A reduction of the water content then renders an insertion more favorable (16).

3.5. Interactions with Different Peptides

A rare but very interesting change in the alignment state of a peptide can be induced by the specific interaction with another peptide. This situation differs from the mere concentrationdependent effect of increasing the number of membrane-bound molecules. For example, magainin 2 and PGLa are known as a synergistic pair of antimicrobial peptides that occur in the same glands of the frog Xenopus laevis. Both of them have been individually shown to undergo a transition from an S-state to a T-state above a critical peptide/lipid ratio, which has been attributed to the formation of homodimers. Interestingly, when combined with magainin 2, PGLa starts to tilt much earlier and it is able to insert fully into the membrane adopting an I-state (16, 80). Correspondingly, in antimicrobial assays a synergistic increase of the activity was observed at a 1/1 molar ratio of PGLa/magainin 2 (95). A likely explanation lies in the formation of synergistically active heterodimers, which have been observed by solution state NMR in detergent micelles (96) (see Fig. 13.7). Other synergistic pairs of antimicrobial peptides have been described, for example,

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Fig. 13.7. Synergistic formation of a stable heterodimeric transmembrane pore by PGLa and magainin 2.

among temporins, also extracted from frog skins. Combinations of either temporin A or B with temporin L have been found to lead to an increase in antimicrobial activity against Gram-negative bacteria (97). Even though the structural basis is not yet resolved, specific interactions between the partner peptides appear to enable their penetration through the outer bacterial membrane, which in the case of Gram-negative bacteria is made of both lipids and lipopolysaccharide.

4. Transitions: Tipping the Balance

So far we have seen that any single membrane-active peptide can display a variable behavior in the way it is folded, and especially how it is spatially embedded and arranged in the membrane. Transitions between different states can be reversible (e.g., between S-, T-, I-states) or irreversible (conversion of an ␣-helical peptide into ␤-amyloid). The different states are usually characterized in separate samples when prepared, e.g., with different P/L ratios, or they are monitored under different conditions, e.g., within a series of experiments at different temperatures. When two states are simultaneously present, it depends on the timescale of interchange and on the experimental method, whether separate populations are detected or a dynamic exchange process leads to time-averaged signals. Both situations have been encountered in solid-state NMR studies of PGLa (9, 11, 12, 16, 80, 85, 86). In view of these intrinsically diverse and dynamic transitions of structures and alignments, which happen in response to changes in the environment, it is clear that the notion of a single mode of membrane interaction may not always be a suitable picture to explain the biological function of a peptide. In the concluding section we now want to address the possible driving forces for transitions between different peptide states.

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Clearly, the system consisting of peptides and lipid has to be treated as a whole, as the mutual interactions between the components are of equal order of magnitude. Nonetheless, it may help to distinguish several scenarios. The behavior of a peptide in the membrane will on the one hand involve interactions with the surrounding lipids as an important contribution. On the other hand, peptide–peptide interactions can be dominant, such that the surrounding lipids play only a minor role. Finally, it may also be conceivable that lipid–lipid interactions are the major player. The important aspect as to what triggers a transition is not necessarily the strength of the interactions involved, but the degree of change when varying the parameter that causes the transition. Considering the initial attraction of a peptide to the membrane surface, electrostatic interactions between the polar lipid headgroups and charged moieties of the peptide are mainly responsible. Hydrophobic interactions then play a role once the peptide is (partially) immersed in the hydrophobic core of the membrane. Important for the tendency to insert more deeply into the membrane are also the elastic properties of the bilayer, modulated, e.g., by the spontaneous curvature of the lipids, and the spatial conformation of the peptide. A theoretical framework to explain the distribution over several peptide states has been established by Heimburg and coworkers (98), expanding on theories of Minton and Chatelier and others (99, 100). To describe the behavior of a membrane-bound peptide, they evaluated the adsorption of a peptide to the bilayer, assuming that the peptide can bind in different states of insertion and alignment to the membrane. One possibility is adsorption to the surface, i.e., in an S-state orientation, without inserting into the bilayer. A second possibility is binding to the membrane in an inserted state. Both modes of binding are characterized by different free energies and different requirements of surface area to accommodate the peptide. Surfacially bound peptides were treated as a two-dimensional gas with a finite area requirement for each particle. When inserted, peptide–lipid interactions lead to an “edge tension,” describing the energetic cost (or gain) of insertion. The lipid area requirement of an inserted peptide, on the other hand, is zero. Using this model, Heimburg and others were able to predict preferential binding in the S-state at low peptide concentration, whereas at high concentration the inserted state prevails. At low concentration, the energetic costs of insertion prevent the peptide from insertion, hence it remains surfacially bound. With an increasing number of adsorbed peptides, the pressure or chemical potential in the two-dimensional surface gas increases and insertion becomes more favorable. Furthermore, inserted peptides present obstacles for S-state binding, decreasing the area available for potential binding sites for S-state peptides, thereby inhibiting any further S-state binding.

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This way, the experimentally observed concentration-dependent change from S-state to an inserted state above a critical peptide to lipid ratio could be well reproduced, as predicted, e.g., by Huang and coworkers (13, 14, 92, 94, 101). Moreover, a pronounced, sharp threshold concentration was obtained when considering oligomeric pores as the inserted state. In this case, higher cooperativity upon insertion, a lower distributional entropy, and a lower area lead to such sharp transitions. Altogether, the pressure of the two-dimensional surface gas formed by the surfacially bound peptides, which would drive insertion, is balanced by the lipid–peptide interactions occurring in the inserted state and resisting insertion. This model is thus able to explain not only concentration-dependent transitions, but also transitions occurring as a consequence of changes in the lipid environment. A temperature variation leading to a change in the lipid phase state, or a different hydrophobic thickness of the membrane leads to a shift of the lipid–peptide interactions, and can therefore shift the concentration threshold to one side or the other. Vice versa, altering the charge distribution of a peptide through, e.g., a pH change will also result in an change of the lipid–peptide interactions. Also Huang has developed a model to explain the transition from a surface-bound state to an inserted state on the basis of the different free energies of these two states (101–103). Similar to the approach of Heimburg above, he assumes peptide binding to the water/membrane interface in two forms, either in the S-state or in a monodisperse oligomeric inserted state. Again, a two-dimensional gas-like behavior is assumed for the S-state. However, differently from Heimburg, in the model of Huang an increase of the membrane area induced by the S-state peptide, and the resulting elastic energy of the membrane is identified as the major contribution to the energy balance of the system. Because of the attractive binding force to the membrane surface, an increase in the interface area between peptide and bilayer surface is energetically favorable. S-state bound peptide thus leads to a stretching of the bilayer, and hence an increase in the elastic energy contribution acting then against further binding in the Sstate. If a critical concentration is exceeded, the balance between elastic forces in the membrane and forces due to the high concentration at the surface is shifted, and the inserted state becomes preferred reducing the elastic energy contribution. Experimental evidence for the model of Huang arises from measurements of the membrane thickness (104). Due to the low compressibility of the membrane, the peptide-induced area increase of the bilayer leads to a thinning of the membrane, which indeed has been observed experimentally in a number of cases. Some experimentally observed transitions between peptide states, however, are not covered by the picture of a lipid–peptide interaction-based binding to the membrane. For example, the

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homo- and heterodimers proposed for PGLa and magainin 2 (on their own and as a pair, respectively), must involve also some specific peptide–peptide interactions and/or entropic contributions of the peptide. Also the temperature-dependent transitions manifested for PGLa are not fully explained by alterations in the lipid– peptide interactions. In the first transition from I-state to T-state near the lipid chain melting temperature, the peptide molecules essentially follow the lipid behavior, but a second transition from T-state to an S-state was observed at higher temperature in fluid membranes. The latter might be ascribed to the disintegration of the putative peptide dimers, pointing again to some peptideoriginating contributions. Even lipid–lipid interactions can under particular circumstances be the driving force for peptides to change their state. In particular at the lipid phase transition many different kinds of peptides have been observed to change their alignment state. For example, gramicidin S is found to insert at temperatures near the lipid phase transition temperature, and high peptide concentrations are able to widen the temperature range of the inserted state to the same extent as they broaden the lipid phase transition itself. A possible explanation are the fluctuations inherent to a phase transition, which lead to local defects in the membrane, which in turn may facilitate peptide penetration. Finally, one might ask critically as to what extent the findings obtained mostly from model membrane systems are able to explain events in actual biological membranes. Could transitions between peptide states be a purely academic exercise, occurring only in synthetic lipid bilayers with their discrete phase transitions and limited compositions? How relevant are the peptide transitions observed at the lipid chain melting temperature, or those peptide states that are found to be stable only in the gel phase? Here, it should be pointed out that the different scenarios encountered in model systems are also found in biomembranes. For example, microdomains possess a more gel-like phase state, and even though a complex membrane has no clearly defined phase transition temperature it may yet be considered as existing within a lipid phase transition over a broad range of ambient temperatures. Hence it is very likely that the diverse behavior of peptides encountered in model systems will also be found in biological systems. Furthermore, any peptide states that can be experimentally observed only when trapped under relatively artificial conditions (e.g., in the gel phase of short-chain lipids) may well occur transiently in native membranes under the impact of concentration gradients or asymmetric membrane binding. Moreover, the tendency of peptides to undergo multiple transitions may well reflect a flexibility that is required to successfully carry out their functions, hence this property appears to be an intrinsic characteristic of membrane-active peptides.

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Chapter 14 Solid-State NMR Investigations of Membrane-Associated Antimicrobial Peptides Christopher Aisenbrey, Philippe Bertani, and Burkhard Bechinger Abstract Solid-state NMR and other biophysical investigations have revealed many mechanistic details about the interactions of antimicrobial peptides with membranes. These studies have shaped our view on how these peptides cause the killing of bacteria, fungi, or tumour cells and how they permeabilize model membranes. As a result, we better understand the biological activities of these peptides and we are now able to design new and better sequences. Here we present some of the tools that have allowed these solidstate NMR investigations, including detailed protocols on how to reconstitute the peptides into oriented or non-oriented membranes as well as simple set-up procedures for 2 H as well as proton-decoupled 31 P or 15 N solid-state NMR measurements. Static and magic angle spinning experiments are described. Where adequate, the special requirements for or limitations of some of the measurements are discussed. Solid-state NMR spectra of both lipids and peptides have been recorded, and through the ensemble of measurements a detailed picture of these complex peptide–lipid supramolecular systems has finally emerged. Key words: Membrane reconstitution, oriented bilayer, helix topology, amphipathic peptide, surface alignment, transmembrane orientation, membrane protein structure, peptide–lipid interactions, pore formation, channel, magic angle spinning.

1. Introduction The investigation ofantimicrobial peptidesby biophysical methods has much enlightened our understanding of the underlying mechanisms of how they interact with membranes, cause membrane permeability increases, and selectively kill bacteria (1). For example, proton-decoupled 15 N solid-state NMR spectra of magainin 2 provided the first indication that these amphipathic A. Giuliani, A.C. Rinaldi (eds.), Antimicrobial Peptides, Methods in Molecular Biology 618, DOI 10.1007/978-1-60761-594-1 14, © Springer Science+Business Media, LLC 2010

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antimicrobial sequences orient parallel to the membrane surface rather than form pores by association into transmembrane helical bundles (2). For other peptides, the issue was unambigously clarified by designing antimicrobial sequences and analysing their behaviour using the same technique (3) in combination with biological assays (4). Biophysical studies have revealed that selected peptides can interact with membranes in a very dynamic and diverse manner, and have shaped our modern view on these systems (reviewed and developed in (1, 5)). To this scope, several solid-state NMR approaches are available each of them with a particular strength. In contrast to solution NMR spectroscopy, where fast molecular tumbling ensures isotropic averaging of the nuclear interactions, in static solid or semi-solid samples the chemical shift, dipolar interactions, and quadrupolar splittings are all dependent on the molecular alignment relative to the magnetic field direction. Therefore, the anisotropy of nuclear interactions is a predominant feature of the NMR spectra also in the case of membraneassociated peptides. On the one hand, fast spinning of the sample around the magic angle (several 1,000 rotations per second at an angle of 54.7◦ with respect to the magnetic field) results in the elimination of many of these anisotropic features, leading to spectra that resemble much those obtained in solution. These so-called magic angle spinning (MAS) solid-state NMR spectra, therefore, reveal small changes in the isotropic chemical shifts and thereby the chemical environments of the nucleus under observation. For example, proton-decoupled 31 P MAS solid-state NMR has been used to follow the selective association of antimicrobial peptides with one component of a mixed membrane (6). Further advantage can be taken from the orientation dependence of NMR interactions in the solid or semi-solid state. The chemical shifts (e.g. 15 N, 13 C, 1 H), quadrupolar interactions (e.g. 2 H and 14 N), or dipolar couplings (e.g. 15 N–13 C and 1 H– 15 N) all depend on the alignment of molecules (and/or bonds) relative to the magnetic field direction. A valuable approach has therefore been to reconstitute peptides and proteins into macroscopically oriented membranes, to insert them in the magnetic field of the NMR spectrometer with the bilayer normal parallel to the magnetic field direction and to record the solid-state NMR spectra. In this manner the 15 N chemical shift, the deuterium quadrupolar splitting, and many other parameters provide orientational constraints and thereby the secondary structure and the alignment of the peptides (7). The sample preparation and the NMR experiments relevant to this approach will be described in Sections 2.2, 3.2, and 3.3 (Fig. 14.1). Furthermore, non-oriented samples, where all directions of the membrane are present and visible in the spectra, result in

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Fig. 14.1. Flow chart for the preparation of samples and the consecutive NMR measurements. The hatched line makes reference to the possibility of investigating oriented samples under MAS conditions (not discussed in the text, see (34, 35)). Typical sample sizes for the analysis of powder pattern line shapes are 10 mg for 31 P or 2 H spectra of lipids and 40 mg for 15 N or 2 H3 NMR spectroscopy of peptides, respectively; for the isotropic chemical shift analysis by MAS solidstate NMR 5 mg of lipids or 10 mg of peptide, respectively; and for oriented samples ≥10 mg of lipid and ≥5 mg of single-site labelled peptide, respectively. Numbers (3.1, 3.2, and so on) refer to main text sections.

broad spectral line shapes which provide valuable information on the motional averaging of the labelled sites, i.e. local motions (8) as well as lateral and rotational diffusion of the molecule as a whole (9, 10). This approach has a long-standing record

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in monitoring the macroscopic phase properties of membranes, by analysing the very different 31 P NMR line shapes of bilayers, hexagonal, micellar, or bicellar phases (11, 12). A more recent analysis of the resulting peptide spectra indicates that these powder patterns represent the alignment of the peptide relative to the membrane normal provided that fast rotation around this axis occurs (9, 13, 14). Samples of peptides associated with membranes made of phospholipids deuterated fatty acyl chains have also been used to analyse the peptide penetration depth, the selective interaction of cationic peptides with anionic lipids in mixed membranes, and the resulting membrane disruptive properties of the sequences (6, 15). The sample preparation and methodology for these NMR approaches will be discussed in Sections 2.1, 3.1, and 3.3 (Fig. 14.1). The theoretical background of solid-state NMR spectroscopy of oriented samples shall not be presented here but a simple correlation exists for ␣-helical peptides that have been labelled with 15 N at one of the amide bonds and which have been reconstituted into oriented or non-oriented membranes (9, 14). In short, it can be shown that for samples that have been uniaxially oriented with the membrane normal parallel to the magnetic field (see Sections 3.2 and 3.3.3), transmembrane ␣helical peptides exhibit 15 N resonances in the 200 ppm range whereas they resonate at 99%, Aldrich), Milli-Q water and isopropanol (industrial grade)/dry ice mixture. For other peptides and lipids

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(see Notes 1 and 2), organic solvents of analytical grade are used, such as hexafluoroisopropanol (HFIP, 99+%, Aldrich), dichloromethane (DCM normapurTM analytical reagent stabilized with 0.1% ethanol, Prolabo/VWR, West Chester, PA, USA), methanol (HPLC grade >99.8%, Fluka, St. Louis, MO, USA), formic acid (purum >98%, Fluka), and acetic acid (Ultra ≥ 99.5%, Fluka). 3. 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC; Avanti Polar Lipids, Birmingham, AL, USA) (see Note 2). 4. Nitrogen gas (bottled or prepared by evaporation of liquid nitrogen). 5. >1.2 mL buffer solution: 150 mM NaCL, 20 mM Tris– HCl, pH 7.4 (see Note 3). 6. NMR sample tubes that fit the NMR coil and probes. For 31 P NMR, Ultra Clear centrifuge tubes (Beckman, Paolo Alto, CA, USA) with home-made Teflon lids have been used in our settings. The 5 mm diameter tubes (175 ␮L volume) fit into a 7 mm MAS rotor after shortening (see Note 4). The next available size is 8 mm which also fits some NMR coils (400 ␮L volume). Depending on the polymer composition, the signal intensity, and the detailed experimental parameters, these plastic tubes result in background signals that can interfere with, e.g., 13 C or 15 N NMR measurements; thus, glass tubes are a better choice (e.g. Verrerie Villeurbannaise, Villeurbanne, France). For MAS or static experiments it is also possible to directly transfer the sample into MAS rotors. Take care when spinning as the lipids act like lubricants that can easily cause loosening of the rotor lid concomitantly with a rotor crash and the loss of the sample. Special inserts or lids are available to reduce these problems (e.g. Wilmad-Labglass, Buena, NJ, USA or high-resolution MAS inserts from Bruker, Rheinstetten, Germany). 7. Access to a solid-state NMR spectrometer (at least twochannels X{1 H} except for 2 H where a single X-channel frequency is applied) with the corresponding probes (solenoidal coil or equivalent): static and/or MAS probes for 31 1 P{ H}, 15 N{1 H}, 13 C{1 H}, and/or 2 H. To investigate the lipid macroscopic phase properties good temperature control is desirable (±1 K). For magic angle spinning solidstate NMR experiments MAS probes and accessories are a prerequisite. 2.2. Peptide Reconstitution into Oriented Membranes

1. Disposable glass tubes ≥10 mL, glass pipettes with long tip for organic solvents, 10 ␮L glass capillaries, 250 ␮L Hamilton syringe, glass Petri dishes with lid (diameter about


215

10 cm), watchmaker forceps, one with pointed and one with flat tips (e.g. Outils Dumont SA, Montignez, Switzerland), Teflon tape, plastic foil that goes with an impulse sealer of the type used in kitchens (e.g. TEW Electrical Heating Equipment, Taipei, Taiwan). 2. Solvents and reagents of analytical grade (see Step 2 of Section 2.1): HCl, 2,2,2-trifluoro ethanol and Milli-Q water. For other peptides and lipids, organic solvents such as hexafluoroisopropanol, dichloromethane, methanol, formic acid, and naphthalene (puriss. for scintillation ≥99% Fluka) can be used (see Notes 1 and 2). 3. 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC; Avanti Polar Lipids) (see Note 2). 4. A few mL each of the following: 1 N NaOH (e.g. normapurTM analytical reagent >85.9% Prolabo/VWR); 200 mM Tris–HCl, pH 7.4; saturated solution of KNO3 (for analysis, min 99%, e.g. Merck, Darmstadt, Germany) in a closed chamber (see Note 5). 5. pH indicator strips covering the range 0–9 in intervals of 0.5. 6. Nitrogen gas (bottled or prepared by evaporation of liquid nitrogen). 7. Ultra thin glass plates that fit your NMR coil (thickness 00 or 0 from Marienfeld, Lauda-Könishofen, Germany). Before preparing the sample test if a stack of glass plates sealed and wrapped in plastic film fits the coil (see Step 8 of Section 3.2 and Fig. 14.2d). Custom-made glass plates of dimensions 11 × 20, 9 × 20 or 8.5 × 20 mm2 have been used in our settings. If you have the choice, 9 × 20 is about half the prize when compared to the 8.5 × 20 size. 8. Access to a solid-state NMR spectrometer (at least twochannels except for 2 H) with the corresponding probes: static 31 P{1 H}, 15 N{1 H}, 13 C{1 H}, 2 H. For better sensitivity during the investigation of peptides in membranes, flat coil-specific NMR probes have been developed (21, 22) and are commercially available from several manufacturers (e.g. Bruker, Rheinstetten, Germany; Varian, Paolo Alto, CA, USA; Doty Scientific, Columbia, SC, USA), although for the investigation of lipids by 31 P{1 H} or 2 H solid-state NMR smaller quantities of sample are required (e.g. a 31 P NMR signal can already be obtained from 10 mg phospholipids oriented between a pair of glass plates) and conventional solenoidal coil shapes have also been used.

216


3. Methods 3.1. Reconstitution of Antimicrobial Peptides into Nonoriented Samples for 31 P or 2 H NMR Spectroscopy of Lipids (Concentration Series of 0–6 mol% Magainin 2 in POPC) (see Notes 6 and 7)

1. In order to remove the TFA counter ions that are usually associated with peptides after cleavage from resins and/or after purification by HPLC, dissolve the peptide at a concentration of 1 mg/mL in 2 mM HCl and lyophilize (23). The cycle of solubilization in 2 mM HCl and freeze-drying should be repeated at least three times (see Note 8). 2. Prepare a stock solution of about 10 mg peptide in 2 mL TFE/100 ␮L H2 O (5 mg/mL). When handling organic solvents use glass ware and avoid contact with plastic and rubber as these may dissolve and/or release organic molecules (see Note 1). 3. Prepare a stock solution of 100 mg of POPC in 2 mL TFE (50 mg/mL) (see Note 2). 4. Mix lipid and peptide solution in glass tubes (or small round bottom flasks) that should have enough volume to accommodate ≥2 mL of solution, position the glass tubes in contact with a warm water bath, and remove the bulk solvent with a gentle stream of nitrogen (see Note 9) in order to deposit a lipid film on the walls of the glass tube, and thereafter expose the film to high vacuum overnight (Table 14.1).

Table 14.1 Example of how stock solutions are mixed to prepare a series of phospholipid membranes with increasing peptide-to-lipid ratio Peptide (mol%)

50 mg/mL lipid stock (␮L) (MW 760)

5 mg/mL peptide stock (␮L) (MW 3,000)

Water (␮L)

TFE (␮L)

1

400

156

57

727

2

400

313

49

578

3

400

470

42

428

6

400

940

0

0

0 (last to be pipetted)

400

0

19

921

5. Hydrate the film with 200 ␮L of buffer (see Note 3) and close the tube with parafilm. Leave for about an hour or longer followed by vortexing. The addition of 3–4 glass beads of about 2 mm in diameter helps in transforming the film into a suspension of multilamellar vesicles (see Note 10). 6. To equilibrate well the samples submit to ≥7 freeze (using dry ice in isopropanol)/thaw (using lukewarm water)/vortex cycles (see Note 11).


217

7. Transfer into sample tubes that fit the NMR coil (see Step 6 of Section 2.1) by using a micropipette. The membranes are sticky, therefore it is necessary to increase the opening of the tip by cutting off the very end. For the same reason it is recommended to transfer several small quantities which avoids the wetting of a large inner surface of the tip. A final centrifugation step allows one to collect the membrane suspension in the bottom of the tube, e.g. by placing the NMR tube in an microcentrifuge tube (e.g. Eppendorf tube) and by slowly spinning in a corresponding centrifuge (e.g. Eppendorf centrifuge at 1,000–2,000 rpm). The inner length of the tubes and/or the positioning of the lids should be adjusted to confine all samples in the centre of the NMR coil. The position in the coil can be stabilized with Teflon tape. For MAS experiments the suspension can be transferred directly into a zirconium MAS rotor (see Section 3.3.4). 3.2. Reconstitution of Antimicrobial Peptides into Oriented Membranes (POPC) for 15 N, 13 C, and/or 2 H Solid-State NMR Measurements of the Peptides (at a Lipid/Peptide Ratio of 50)

1. In order to remove the TFA counter ions that are usually associated with peptides after cleavage from resins and/or after purification by HPLC, dissolve the peptide at a concentration of 1 mg/mL in 2 mM HCl and lyophilize (23). The cycle of solubilization in 2 mM HCl and freeze-drying should be repeated at least three times (see Note 8). 2. Dissolve about 12 mg peptide in 2 mL TFE in a glass tube which leaves sufficient space for subsequent manipulations (e.g. 10 mL). 3. Adjust pH to approximately neutrality by the successive additions of small amounts of 1 N NaOH (5–10 ␮L at a time). The presence of 70 ␮L of 200 mM Tris–HCl, pH 7.4, helps during the titration (but see Note 3). The pH is controlled after each addition of base by removing small quantities of peptide solution using a 10 ␮L capillary and the application of a small droplet of this solution onto pH indicator paper. Once the organic solvent has evaporated a drop of Milli-Q water is added to read out the pH from the colour change (see Note 12). 4. Add 150 mg of POPC to the solution (see Note 13). 5. Concentrate the solution until it turns viscous (to about 1 mL) by using a gentle stream of nitrogen (see Note 9), in order to be able to deposit small droplets that stick to the glass plates in the next step. 6. Carefully place about 30 clean ultra-thin microscope cover glasses side by side on two or three glass Petri dishes. Use fine watchmaker forceps to manipulate the glass plates. Apply equal quantities of the previous solution as small elongated droplets onto the central areas of all but one glass

218


A

B

C

D

Fig. 14.2. The final steps of the preparation of oriented membrane samples are illustrated. (a) Application of viscous lipid/peptide solutions onto ultra-thin cover plates. (b) After elimination of the organic solvent and rehydration the gas plates are stacked on top of each other. (c) The sample is sealed into plastic foil and inserted into a flat coil solid-state NMR probe for measurement (d).

plates using a Hamilton syringe (Fig. 14.2a). Keep one glass plate on the side to be used during the stacking of the plates (during Step 8). Let the sample dry in air until most of the solvent has evaporated. It is possible to apply several layers onto the same regions when necessary. After the sample has been equally distributed and the bulk solvent has evaporated in air, expose the sample to high vacuum overnight. In our own laboratory we have connected a desiccator to the lyophilizer to allow the drying of many samples simultaneously in their horizontal position. 7. Thereafter the samples are placed in a closed chamber at 93% relative humidity (rh) and left to equilibrate for typically about 3 days. This can be achieved by establishing a closed atmosphere in contact with a KNO3 saturated solution (see Note 5). 8. Once the lipid films become translucent and soft (see Note 5) the glass plates are stacked on top of each other, with one empty glass plate used to cover the last top surface (Fig. 14.2b). Membrane alignment can be improved


219

by shearing with delicate pressure and small movements. The stack is stabilized by wrapping with Teflon tape and the whole sample sealed in a plastic wrapping using an impulse sealer (Fig. 14.2c). The volume of the sample should fit tightly into the NMR coil (see Step 8 of Section 2.2 and Fig. 14.2d). 3.3. NMR Measurements

3.3.1. 2 H Solid-State NMR Spectra (Oriented or Non-oriented)

In this paragraph the set-up procedure for three types of measurements is described. However, it is assumed that the beginner receives a hands-on introduction into the use of a solidstate NMR spectrometer, as well as the computer and pulse programmes. The latter should be installed and tested by an experienced user. Beware of the dangers associated with the high-field magnet and the high operating voltage of the electronic equipment. Some simple set-up procedures and pulse sequences such as standard 1 H acquisition, Hartmann–Hahn matching, or crosspolarization are also explained in an applications-oriented manner in reference (24). 1. Insert a sample of D2 O into the centre of the NMR coil. Close the probe head and insert the probe into the NMR magnet. With the amplifiers silent connect the 2 H (Xchannel) electronic circuit of the probe to the console. During operation this line carries incoming radio frequency (RF) pulses from the console to the probe and outgoing signal from the sample via the preamplifier (that is tuned to the 2 H Larmor frequency) to the detector. 2. Tune and match the probe for the 2 H carrier frequency. 3. Using a simple pulse acquisition sequence does vary the pulse length to determine the maximal and the zero intensities (90◦ and 180◦ pulses, respectively). Adjust the carrier frequency to have the signal close to the centre of your spectral window and all the other parameters according to Table 14.2. Adjust the receiver gain to avoid saturation and good sensitivity at the same time. Using a short pulse, adjust and save the phases to have a pure positive signal intensity (Lorentzian). Calibrate the chemical shift scale by setting the maximum of the D2 O signal to 0. Adjust the power of the pulses to have a 90◦ pulse in the range of ≤ 5 ␮s. Once these parameters have been determined for a given spectrometer and probe, they provide a valuable starting point for future set-up procedures, which should then require only minor readjustments. 4. Using the 2 H power levels determined in Step 3 adjust the durations of a 90x –τ –90y –τ acquisition pulse programme (25), which is presented schematically in Fig. 14.3a. Adjust the 90◦ pulse as determined and all the other parameters

220


Fig. 14.3. Solid-state NMR pulse sequences and typical spectra of lipids and peptides: (a) Deuterium quadrupolar echo ◦ sequence where the phase of the pulse and receiver are cycled in the following manner (25): First 90 : x -y -x y ◦ x -y -x y; second 90 : -y -x y x y x -y -x; acquisition: y x -y -x y x -y -x (25). To the right of the pulse sequence are shown membrane fragments that are oriented randomly and in which are incorporated helical peptides. Furthermore, a motionally averaged 2H powder pattern line shape of peptides labelled with 2 H3 -alanine is shown. (b) 31 P Hahn-echo sequence with proton decoupling (26). Typical spectra of unoriented and (partially) oriented samples are shown to the right together with an illustration of the phospholipid alignment. The phase cycles of the pulses and the ◦ ◦ receiver are (26): 90 : x y -x -y x y -x -y -x -y x y -x -y x y; 180 : y x y x -y -x -y -x x y x y ◦ 1 15 -x -y -x -y; acquisition: x y -x -y. (C) H- N cross-polarization experiment. The 90 -1 H pulse is phase shifted by 1 ␲/2 relative to the phase of the subsequent H CP contact pulse. Oriented membranes carrying in-plane oriented (top) or transmembrane helical peptides (bottom) are schematically illustrated and typical 15 N spectra resulting from such configurations are shown to the right.

according to Table 14.2. Using the reference sample the performance of the pulse programme can be tested by adding a full-phase cycle (eight scans). Check that the oscillations (free induction decay, FID) recorded from each repetition add to the overall signal intensity, and for the absence of artefacts in its beginning (probe ringing may require longer τ ) and of spikes (cleaning the coil may help). With some spectrometers, an installed lock unit may interfere with the signal. This problem can be solved by reducing/turning off the lock power. Stably insert the membrane sample into the centre of the NMR coil (see Note 4). Reconnect the probe, tune, and match (Steps 1 and 2) for every new sample and after equilibrating to a new temperature. Use the parameters determined before


221

(Table 14.2). Readjust the receiver gain for the lipid sample to obtain the maximal sensitivity without saturating the receiver. The signal should become visible within minutes (lipids) to a few hours (peptides), and it should be possible to obtain a spectrum with reasonable signal-to-noise ratio in about 30–60 min (lipids) or overnight (peptides). Note that the signal from naturally abundant deuterium in water shows up first and can be reduced by using deuterium-depleted water for sample hydration. 3.3.2. Proton-Decoupled 31 P Solid-State NMR Spectra (Oriented or Non-oriented)

1. Insert a sample of 85% H3 PO4 into the centre of the NMR coil. Close probe head and insert the probe into the NMR magnet. With the amplifiers silent connect the 31 P (X) and the 1 H electronic circuits of the probes to the respective electrical connections to allow during the following steps passage of incoming RF pulses from the console and outgoing signal from the sample via filters and the preamplifier that covers the 31 P Larmor frequency. 2. Tune and match the probe (31 P and 1 H electronic circuits). 3. Using a simple pulse acquisition sequence vary the pulse length to determine the maximal and the zero intensities (90◦ and 180◦ pulses, respectively). Using an isotropic liquid during this set-up procedure renders 1 H decoupling unnecessary, and it can even heat and damage the sample and/or probe head as long acquisition times are used to fully record the free induction decay. Adjust the carrier frequency to have the signal close to the centre of your spectral window and all the other parameters according to Table 14.2. Adjust the receiver gain to avoid saturation and good sensitivity at the same time. Using a short pulse, adjust and save the phases to have a purely positive signal intensity. Calibrate the chemical shift scale with the maximum of the phosphoric acid signal at 0. Adjust the power of the pulses to have a 90◦ pulse in the range of 5 ␮s. Once these parameters have been determined for a given spectrometer and probe, they provide a valuable starting point for future set-up procedures, which should then require only minor re-adjustments. 4. Change the spectrometer settings to acquire the 1 H signal. Adjust the power levels of the 1 H channel to have a 90◦ pulse length ≤7 ␮s and the 1 H carrier frequency using a procedure analogous to the previous step. This step is required only once in a while to measure or control the 1 H decoupling field strength and the 1 H frequency. 5. Using the 31 P and 1 H power levels determined in Steps 3 and 4 adjust the durations of the 90◦ –τ –180◦ –τ (acquisition with 1 H decoupling) pulse programme (26) graphically represented in Fig. 14.3b. Adjust the 90◦ and 180◦ pulses as determined and all the other parameters according to Table 14.2. Using the reference sample the performance of

n.a. 10 kHz 1 51 ms

τ delay

Spectral width

Number of scans (typical values)

Acquisition time

4 6 ms


Acquisition time

n.a. – not applicable.

Reference frequency

39.3 ppm @

20 kHz

Receiver settings

1 ms

Spectral width

(≤ 8 ␮s)

Cross-polarization contact time

/ 5s

H power level and 90 pulse length

Idem

6 ms

5,000/50,000

100 kHz

40 ␮s

0.3 s/1.5 s

n.a.

Idem

H echo lipid/2 H3 -alanyl

2

Hz

H–15 N cross-polarization NH4 Cl powder

15

1

Hz

Recycle delay (see Note 14)

1

Experiment and substance

Section 3.3.3

Reference frequency

0 Hz @

1s

Receiver settings

n.a.

(≤6 ␮s)

180 pulse length

/

Pulse acqu. 2 H2 O


Power level/90◦ pulse


Section 3.3.1

max @

200 ms

1

Hz

(≤7 ␮s)

40 kHz

n.a.

2s

/

Pulse acqu. 85% 1 H3 PO4

Section 3.3.2

␮s

Idem

10 ms

1,024

40 kHz

40 ␮s

2s

Idem

Idem

P echo liquid disordered membranes

Idem

3 ms

20,000

40 kHz

1 ms

3s

Idem

H–15 N cross-polarization peptide

1

0 Hz @

32 ms

1

Hz

(≤6 ␮s)

30 kHz

n.a.

2s

/

Pulse acqu. 85% H3 31 PO4

31

Table 14.2 Typical solid-state NMR acquisition parameters for experiments on static samples. Use a copy of the table to keep track of your own values

222 Aisenbrey, Bertani, and Bechinger


223

the pulse programme can be tested by adding a full-phase cycle (16 scans). Check the FID for being additive from scan to scan, and for the absence of artefacts in its beginning (probe ringing may require longer τ ) and of spikes (reduction of the decoupling power and/or cleaning the coil may help). 6. Stably insert the sample into the centre of the NMR coil (see Note 4). Reconnect the probe, tune, and match (Steps 1 and 2) for each new sample and after equilibrating to a new temperature. Use the same parameters as before (Table 14.2) but reduce the recycle delay to 1.5–3 s. Readjust the receiver gain for the lipid sample for maximal sensitivity without saturating the receiver. The signal should become visible within minutes, and it should be possible to obtain a spectrum with good signal-to-noise ratio in about 30 min (for a sample size of 10 mg of phospholipid). 3.3.3. Proton-Decoupled 15 N Cross-Polarization Solid-State NMR Spectra (Oriented or Non-oriented)

1. Using a reference sample of 15 NH4 Cl follow the Steps 1 and 2 in Section 3.3.2 in an analogous manner using the 15 N and 1 H electronic circuits. An analogous procedure to the one described here can be applied to set up 15 N/1 H crosspolarization experiments using adamantane. 2. Adjust the power levels of the 1 H channel to have a 90◦ pulse length ≤7 ␮s and the 1 H carrier frequency using a simple pulse acquisition sequence analogous to Step 3 of Section 3.3.2 (see Note 15). 3. Switch to the acquisition of the 15 N signal. It is recommended to use a cross-polarization sequence (24) with the possibility to vary the power levels of the 90◦ 1 H pulse, the 1 H and 15 N contact pulses and the 1 H decoupling independently (Fig. 14.3c). Keep the 1 H power level fixed as determined in Step 2 for all intervals (90◦ pulse, contact time, and decoupling during acquisition), set the length of the 90◦ 1 H pulse as determined, choose a contact time of ≤ 5 ms, and vary the power level of the 15 N channel to obtain the maximal intensity (see Note 15). Once you obtain signal adjust the 15 N carrier frequency to have the signal close to the centre of your spectral window, correct, and save the phases for a positive 15 N signal. In case major corrections of the frequencies had to be made check and re-adjust the power levels for maximal signal intensity. Use the parameters according to Table 14.2. Adjust the receiver gain to avoid saturation and permit good sensitivity at the same time. Calibrate the chemical shift scale with the maximum of the ammonium peak at 39.3 ppm. Once these parameters have been determined for a given spectrometer and probe, they provide a valuable starting point for future set-up procedures, which

224


should then require only minor corrections. By constantly comparing the noise level and the signal intensity with previous settings using the same reference sample, it is possible to keep track of the performance of the probe and the spectrometer. 4. Using the reference sample the performance of the pulse programme can be tested by adding a full-phase cycle (typically, eight scans). Check the growing FID for being additive from scan to scan. 5. Stably insert the sample into the centre of the NMR coil, tune, and match the 15 N and 1 H channels for each new sample. 6. Switch to the acquisition of 1 H. Record the 1 H NMR spectrum of the sample and adjust the 1 H power levels to obtain the same 90◦ /180◦ pulse length as determined in Step 2 and used during Step 3. Depending on the content of water and salt significant increases in power may be necessary (typically by 1–3 dB) to obtain the same probe performance (i.e. effective B1 field). 7. Switch to the cross-polarization pulse programme and switch the spectrometer to the acquisition of 15 N. Adjust the following parameters by keeping the previous 15 N settings, but by using the new 1 H power levels: 90◦ 1 H pulse as determined in Steps 2 and 6, contact time 0.8–1 s, spectral width 40 kHz, and an acquisition time of about 3 ms (Table 14.2). Adjust the receiver gain to avoid saturation and permit good sensitivity at the same time. Use the chemical shift calibration of Step 3. Check the first acquisitions (mostly noise) for the absence of artefacts in its beginning and spikes throughout the FID (reduction of the decoupling power and/or cleaning the coil may help). During acquisition the sample should be cooled with a stream of air, which can be humidified by bubbling through a gas wash bottle provided that acquisition is at ≥ room temperature (if the temperature of the water bath is above that of the connecting lines and probe water condensation will occur at the colder sites). It is recommended to check the tuning of the 1 H channel after a few hours of accumulation as water loss or redistribution within the sample can occur due to RF heating. 3.3.4. Magic Angle Spinning Experiments 3.3.4.1. Transferring Crystalline or Nano-crystalline Solids into the MAS Rotor

1. Powder the sample finely with mortar and pestle. 2. Transfer the sample into the NMR rotor (e.g. zirconium) using the appropriate funnel in several steps and compress between the steps. To ensure stable spinning, a long life of the probe head stator and sensitivity the sample should be homogeneously filled and positioned in the middle of the


225

coil. If there is not enough sample available the use of inserts allows one to centre the sample in the middle of the rotor. 3. Close the sample with the appropriate cap (e.g. Kel F; however, if the rotor or cap material creates background signals other material should be chosen) and make sure that the cap is properly inserted and fits tightly the rotor. 3.3.4.2. Transferring Wet or Soft Solids (Membrane Samples) into the MAS Rotor

1. Transfer the sample with a spatula into the rotor in several steps. Pellet the sample into the rotor in between steps using a microfuge (e.g. Eppendorf centrifuge). Special homemade devices can be prepared to directly centrifuge the sample into the rotor. 2. Close the rotor with the appropriate cap (see Step 3 of Section 3.3.4.1). Use lids or specially designed inserts for wet samples to avoid the accidental opening of the rotor during rotation (see Step 6 of Section 2.1).

3.3.4.3. Setting up Proton-Decoupled 13 C or 15 N CP/MAS Spectra

1. Set the magic angle following the manufacturers’ instructions. Usually this is done by maximizing the sideband intensities of KBr or NaNO3 spectra or the rotational echoes (spikes) on the FID. Once this calibration has been performed it is usually stable over long time periods. 2. Insert the reference sample (natural abundance adamantane for 13 C, 15 NH4 Cl for 15 N, natural abundance 85% phosphoric acid or phosphoserine for 31 P). The changes in the proton wobbling curve can be used to follow the insertion process. 3. Start spinning following manufacturer’s instructions. Start slowly to allow the sample to pack into the rotor under centrifugal forces. The 1 H wobbling curve and MAS spinning frequency can be used to monitor spinning stability. 4. Set the spinning speed at the desired value respecting probe head and rotor specifications. 5. Tune and match both channels of the probe head. 6. Follow Steps 2–7 of Section 3.3.3 using typical values reported in Table 14.3 to set up cross-polarization experiments using adamantane or 15 NH4 Cl (see Note 15). Follow Steps 1–4 of Section 3.3.2 and the values reported in Table 14.3 for the set-up of 31 P NMR spectra using 85% H3 PO4 under non-spinning conditions. Under MAS conditions the spectra of the lipids are acquired using a simple 90◦ (acquisition with 1 H decoupling) sequence.

300 ms, reduce decoupling power!!!!

Acquisition time


Acquisition time

Reference frequency

Hz

4


38.5 and 29.5 ppm @

40 kHz

Receiver settings

1 ms

Spectral width

(≤8 ␮s)


/ 5s


H–13 C cross-polarization adamantane powder

1


1


Reference frequency

Hz

4


39.3 ppm @

40 kHz

Receiver settings

1 ms


(≤ 8 ␮s)

Spectral width

/ 5s


H–15 N cross-polarization NH4 Cl powder

15

1


1


Section 3.3.4

Idem

30 ms

1,024

40 kHz

1 ms

5s

Idem

H–13 C cross-polarization peptide

1

Idem

30 ms

1,024

40 kHz

1 ms

5s

Idem

H–15 N cross-polarization peptide

1

Table 14.3 Typical solid-state NMR acquisition parameters for experiments under MAS conditions. Use a copy of the table to keep track of your own values

226 Aisenbrey, Bertani, and Bechinger

n.a. – not applicable.

Reference frequency

0 ppm @

Hz


Acquisition time

Receiver settings

20 kHz 4


n.a.


(≤8 ␮s)

Spectral width

10 s

/

P simple acquisition H3 PO4

31

H power level and 90 pulse length t Recycle delay (see Note 14)

1


Table 14.3 (continued)

100 ms

1,024

25 kHz

n.a.

3s

Idem

H-decoupled 31 P phospholipid sample

1

Solid-State NMR of Membrane Peptides 227

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4. Notes 1. It is pivotal to find a solvent system where peptides, lipids, and other constituents are homogenously mixed. For amphipathic peptides this can usually be achieved in binary and ternary mixtures of DCM, TFE, and water (e.g. 1.2/1.8/0.3), DCM/methanol or in 2 mL HFIP or formic acid (18). The solubility of cationic sequences is usually larger in acidic environments, and solubilization can be accelerated by vigorous mixing or sonication. The use of simple systems made up of only one (or two) volatile solvent is advantageous. In multi-component solvent mixtures the more volatile solvents, such as DCM, evaporate earlier and phase separations may occur. In these instances this solvent can be re-added during the drying process. Also, in some instances it has been observed that suspensions form during the drying process, which in most cases was without detrimental effect on the quality of the sample alignment (see Section 3.2). 2. Often it is desired to test the effect of membrane lipid composition on the peptide–lipid interactions. On one hand POPC represents well the phospholipid composition of many biological membranes, as the PC head group is abundant in the bilayers of higher organisms. The composition of these membranes is furthermore mirrored by a saturated fatty acyl chain at position 1 and an unsaturated chain at position 2 and POPC represents well their average hydrophobic thickness. Furthermore, the negative charges of eukaryotic membranes are often carried by PS, and these membranes are also rich in cholesterol. On the other hand, a simple bacterial membrane mimic could be PE/PG 3:1. Notably, however, many of these lipid components exhibit low solubility in alcohols. Therefore, dichloromethane (or chloroform) provides an alternative for most long-chain lipids (cf., for example, the catalogue information by Avanti Polar Lipids). 3. A wide variety of buffers can be used including Tris, HEPES, or citrate buffer. However, the interference of the buffer with the NMR experiments should be considered. For example, phosphate buffers result in large isotropic peaks hampering the analysis of 31 P NMR powder patterns, water contains a significant amount of deuterium (which can be reduced by using deuteriumdepleted water), and other buffers cause background signals in 13 C NMR experiments. Furthermore, high salt


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concentrations interfere with the tuning of NMR probes and the radio frequency irradiation during NMR spectroscopy. Also, extreme pH values cause the hydrolysis of ester bonds and thereby lipid degradation. Long-term stability of lipids can be assured by working at pH 6–7 (27), reduced hydration and/or storage in the freezer. When oriented samples are prepared at 95% peptide purity. The S3 34’mer sequence N-HAEHKVKIGVEQKYGQFPQGTEVTYTCSGNYFLMC, with a molecular weight of 3,892, corresponds to residues 268–301 of Factor C and Sushi 3 domain (GenBankTM/EBI accession number S77063). 2. Many types of cantilevers and tips are available on the market. Most of them are microfabricated from silicon or silicon nitride. Generally speaking, silicon tips are usually cone shaped and silicon nitride tips are pyramid shaped. A reasonable sharp tip (tip radius < 10 nm) with small open angle and high resonance frequency (200–300 kHz) is found suitable for bacteria imaging in air. 3. One of the significant issues of imaging in air is the influence of a thin layer of water present on the surface of both tip and sample, which gives rise to the so-called meniscus effect and the resultant strong adhesion force can trap the

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Fig. 15.4. Three-dimensional AFM height images and the corresponding cartoons of proposed S3–Gram-negative bacteria interactions. (A) Control normal cell. (B) Low-concentration treatment with S3 (arrow indicates the formation of micelle of LPS–S3 complex). (C) Medium-concentration treatment with S3 (arrow indicates the leakage of intracellular materials). (D) High-concentration treatment with S3 (dotted red line circles a totally lysed cell surrounded by masses of intracellular materials and cell debris). Specimen was prepared as described in Section 3.2

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tip on the surface and cause unstable imaging. Thus, controlling the environment humidity below 50–60% will be helpful. 4. It is useful to prepare a standard curve by plotting the OD600 of different dilutions of the test culture against the colony forming units per mL. Correlate the average OD600 of the overnight test culture with the standard curve to determine the culture cell number. 5. If the sample gets dried up in the culture solution, the salt crystals and impurities from the solution will severely contaminate the sample surface. Thus, make sure no saltcontaining solutions are left on the glass slide surface. Moreover, no fixation is needed since the cell wall structure prevents the cell from collapsing during the drying process and fixation may introduce artifact on the ultrastructure. However, keeping cells in ultrapure water exerts osmotic pressure on the cells and will eventually lyse the cells. So try to minimize the duration of incubation in ultrapure water and carefully compare with the control (same incubation time in ultrapure water but no peptide treatment) for proper interpretation. If a specific bacterial culture – such as some Gram-positive bacterial species – cannot be kept in ultrapure water, other preparation methods may need to be adapted and used. 6. A completely dried sample is critical for obtaining reliable AFM imaging, but fast drying methods such as heating may not be optimized for this application as they make the cells dehydrate too quickly and can cause the cell wall to collapse. Drying under nitrogen flow may achieve the same results as that of a vacuum desiccator. 7. If laser is correctly aligned but no signal appears on the photodiode screen, either there is a problem with the reflective side of the AFM cantilever or the signal falls out of the detectable area of photodiode. In such a case, adjust the two screws for photodiode detector positioning to get the signal back or, in some types of fixed photodiode, adjust the mirror in between the tip and photodiode to get the signal back to the photodiode screen. 8. If a warning of exceeding safety driving amplitude range appears, check the sweeping range to make sure it is within the estimated resonance frequency indicated by manufacturer (normally, set the range between 100 and 500 kHz). Also, there could be a laser misalignment problem where the laser was aligned onto the chip instead of cantilever, or a tip positioning problem where tip is not fixed well onto the tip holder. In such a case, try to realign the laser or

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reload the tip onto the tip holder. If the “autotune” function is not available in the software, one can manually tune the cantilever under oscilloscope mode. Refer to the specification of the cantilever from the manufacturer and find the right peak from oscilloscope mode with target amplitude set to 1 V. Choose the working frequency at about 10–20% shift left to the resonance peak and set point at 70–80% of the target amplitude. Tuning check should be performed after several images are captured to avoid any contamination-induced resonance peak shift and the subsequent imperfect performance. 9. Monitor the cross section trace lines in height channel and adjust gains and set point step by step to achieve closely matched traction and retraction curves. Gains should be maximized to track effectively the surface features while set point should be set at a high level (tapping force is kept low) to avoid sample destruction and distorted imaging arising from high tapping force. 10. This step is very important to exclude any tip-induced artifact in imaging. As it can be seen in Fig. 15.3, a bad tip may give rise to a faulty image without user’s realization. 11. Small-scale imaging may require readjustment of parameters (smaller gains and faster scan speed) for optimization. Check different sample sites to confirm the uniformity of the observed structures.

Acknowledgments We thank Mr. Han Chong Ng for the preparation of the bacterial cultures and Ms. Pei Yun Lee for the assistance on AFM imaging and discussion. This work was funded by the Singapore-MIT Alliance (SMA2) and MoE Tier 2 grant (J.L. Ding and B. Ho). References 1. Gordon, Y. J., Romanowski, E. G., and McDermott, A. M. (2005) A review of antimicrobial peptides and their therapeutic potential as anti-infective drugs. Curr. Eye Res. 30, 505–515. 2. Sang, Y. and Blecha, F. (2008) Antimicrobial peptides and bacteriocins: alternatives to traditional antibiotics. Anim. Health Res. Rev. 9, 227–235. 3. Zasloff, M. (2002) Antimicrobial peptides of multicellular organisms. Nature 415, 389–395.

4. Ding, J. L., Li, P., and Ho, B. (2008) The Sushi peptides: structural characterization and mode of action against Gram-negative bacteria. Cell. Mol. Life Sci. 65, 1202–1219. 5. Tan, N. S., Ng, M. L., Yau, Y. H., Chong, P. K., Ho, B., and Ding, J. L. (2000) Definition of endotoxin binding sites in horseshoe crab factor C recombinant sushi proteins and neutralization of endotoxin by sushi peptides. FASEB J. 14, 1801–1813. 6. Li, P., Wohland, T., Ho, B., and Ding, J. L. (2004) Perturbation of lipopolysaccharide

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8. 9.

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(LPS) micelles by Sushi 3 (S3) antimicrobial peptide. The importance of an intermolecular disulfide bond in S3 dimer for binding, disruption, and neutralization of LPS. J. Biol. Chem. 279, 50150–50156. Li, P., Sun, M., Wohland, T., Ho, B., and Ding, J. L. (2006) The molecular mechanism of interaction between sushi peptide and Pseudomonas endotoxin. Cell. Mol. Immunol. 3, 21–28. Binnig, G., Quate, C. F., and Gerber, C. (1986) Atomic force microscope. Phys.l Rev. Lett. 56, 930–933. Li, A., Lee, P. Y., Ho, B., Ding, J. L., and Lim, C. T. (2007) Atomic force microscopy study of the antimicrobial action of Sushi peptides on Gram negative bacteria. Biochim. Biophys. Acta. 1768, 411–418. Zhong, Q., Inniss, D., Kjoller, K., and Elings, V. B. (1993) Fractured polymer/silica fiber surface studied by tapping mode atomic force microscopy. Surf. Sci. Lett. 290, 688–692. Suo, Z., Yang, X., Avci, R., Kellerman, L., Pascual, D. W., Fries, M., and Steele, A. (2007) HEPES-stabilized encapsulation

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of Salmonella typhimurium. Langmuir 23, 1365–1374. da Silva, A., Jr. and Teschke, O. (2003) Effects of the antimicrobial peptide PGLa on live Escherichia coli. Biochim. Biophys. Acta. 1643, 95–103. Meincken, M., Holroyd, D. L., and Rautenbach, M. (2005) Atomic force microscopy study of the effect of antimicrobial peptides on the cell envelope of Escherichia coli. Antimicrob. Agents Chemother. 49, 4085–4092. da Silva Junior, A. and Teschke, O. (2005) Dynamics of the antimicrobial peptide PGLa action on Escherichia coli monitored by atomic force microscopy. World J. Microbiol. Biotechnol. 21, 1103–1110. Braga, P. C. and Ricci, D. (1998) Atomic force microscopy: application to investigation of Escherichia coli morphology before and after exposure to cefodizime. Antimicrob. Agents Chemother. 42, 18–22. Dufrene, Y. F. (2008) Atomic force microscopy and chemical force microscopy of microbial cells. Nat. Protocols 3, 1132–1138.

Chapter 16 Fluorescence and Electron Microscopy Methods for Exploring Antimicrobial Peptides Mode(s) of Action Ludovica Marcellini, Maria Giammatteo, Pierpaolo Aimola, and Maria Luisa Mangoni Abstract Due to the increasing resistance of microbial pathogens to the available drugs, the identification of new antimicrobial agents with a new mechanism of action is urgently needed. In this context, cationic antimicrobial peptides (AMPs) are considered promising candidates. Although there is evidence that, in contrast to conventional antibiotics, microbial membranes are the principal target of a large number of AMPs, thus making it difficult for the pathogen to acquire resistance, their mode(s) of action is not yet completely clear. Intense research is currently devoted to understand the effect(s) of AMPs on intact cells, either at sub-lethal or at lethal peptide concentrations, and fluorescence/electron microscopy techniques represent a valid tool to get insight into the damage caused by these molecules on the morphology and membrane structure of the target cell. We here present an overview of some microscopic methodologies to address this issue. Key words: Antimicrobial peptides, mode(s) of action, fluorescence microscopy, scanning electron microscopy, transmission electron microscopy, membrane permeation.

1. Introduction The discovery of new anti-infective formulations has become a pressing necessity, because of the growing emergence of pathogenic microorganisms that have acquired resistance to a wide range of commercially used antibiotics. Natural antimicrobial peptides (AMPs), which are produced by almost all living forms, act as the first line of defense against noxious invaders (1–5), and represent attractive molecules for the design and A. Giuliani, A.C. Rinaldi (eds.), Antimicrobial Peptides, Methods in Molecular Biology 618, DOI 10.1007/978-1-60761-594-1 16, © Springer Science+Business Media, LLC 2010

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manufacture of new peptide-based antibiotic therapies (6). Studies aimed at elucidating the effects caused by AMPs on the permeability of the target cell membrane and the correlation between membrane perturbation/surface structure and microbial viability will certainly contribute to broaden our knowledge on the mode(s) of action of AMPs on intact cells. For this purpose, a useful tool is represented by fluorescence and electron microscopy techniques. 1.1. Fluorescence Microscopy (Triple-Staining Method)

Fluorescence microscopy allows to image cells and/or intracellular components, by labeling with specific fluorophores. We developed a triple-staining method to visualize the effects of a shortsized AMP from frog skin (namely, temporin L; see 7) on the viability and membrane integrity of individual Escherichia coli cells. This method is based on the following fluorochromes: (i) the vital dye 5-cyano-2,3-ditolyl tetrazolium chloride (CTC), to stain metabolically active microorganisms. CTC is a monotetrazolium redox dye, which is colorless and nonfluorescent unless it is exposed to an electron-transport chain. Indeed, in respiring cells, CTC is readily reduced to a red fluorescent formazan salt that accumulates intracellularly (8, 9); (ii) the DNA-binding dye 4,6-diamidino-2-phenylindole (DAPI), which stains all bacterial cells irrespective of viability. DAPI binds to a double-stranded DNA, forming a stable complex which gives a blue fluorescence when excited by UV light; (iii) the low molecular mass (389.4 Da) green fluorescent probe fluorescein isothiocyanate (FITC), which is unable to traverse the cytoplasmic membrane of intact cells unless this is damaged by a permeabilizing agent. This probe is used to assess alterations in the membrane permeability. The combination of the double CTC–DAPI staining with FITC allows to simultaneously identify in a single preparation the total number of bacteria (cells with a blue fluorescence, due to DAPI binding to DNA), the bacteria with an altered membrane permeability (cells with a bright green fluorescence, due to FITC uptake), and the metabolically active bacteria (cells with a red fluorescence, due to formation of CTC–formazan crystals) (7). Interestingly, this technique permits to screen peptides or other molecules that are able to modify the membrane permeability of microbial cells without affecting their viability (as detected by the emission of both green and red fluorescence). In addition, the triple-staining method permits to identify bacteria in which the killing process and/or membrane

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permeation causes DNA leakage (revealed by absence of blue fluorescence). 1.2. Scanning and Transmission Electron Microscopy

With reference to electron microscopy, both scanning electron microscopy (SEM) and transmission electron microscopy (TEM) represent valid techniques to provide information on the effects caused by AMPs on microorganisms, at higher resolution than optical microscopy. In particular, SEM allows to investigate changes in the morphology of the sample’s surface (e.g., surface of the microbial cell), whereas TEM allows to shed light into the effects induced by AMPs on cellular components at the ultrastructural level (e.g., membrane damage).

2. Materials 2.1. Triple-Staining Procedure 2.1.1. Bacterial Culture

1. Luria-Bertani (LB) broth: 1% (w/v) bacto tryptone, 0.5% (w/v) NaCl, and 0.5% (w/v) yeast extract (Oxoid, LTD, Basingstoke, UK) in distilled water. The final pH has to be adjusted to 7.4 with 1 N sodium hydroxide (NaOH). Using a graduated cylinder, dispense aliquots into glass bottles, autoclave them at 120◦ C for 20 min, and store the sterilized medium at room temperature (rt). 2. 10 mM sodium phosphate buffer, pH 7.4 (NaPB): stock solution of 100 mM NaPB is prepared by mixing 77.4 mL of 1 M Na2 HPO4 with 22.6 mL of 1 M NaH2 PO4 while stirring. Both monobasic and dibasic sodium phosphates are dissolved in distilled water (see Note 1). Working buffer is prepared by diluting the stock solution 1:10 in distilled water. Sterilize by filtration (0.45-␮m filters). 3. 24-well polystyrene Costar plates (Corning, Acton, MA, USA). 4. Spectrophotometer (e.g., UV-1700 Pharma Spec from Shimadzu, Kyoto, Japan). 5. Thermomixer (e.g., Eppendorf, Barkhausenweg, Germany).

2.1.2. Poly(l-lysine)-Coated Cover Glasses

1. Microscope cover glasses (12 mm diameter). 2. Petri dishes (10 cm diameter). 3. Alkaline wash solution: 10% (w/v) NaOH + 60% (v/v) ethanol (see Note 2). Use distilled water to prepare both NaOH and ethanol solutions before mixing. 4. Poly(L-lysine) 70,000–150,000 Da (Sigma, St. Louis MO, USA) (0.1 mg/mL in distilled water). 5. Pure ethanol.

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2.1.3. Buffers and Fluorescent Probes

1. Phosphate-buffered saline (PBS): 10 × stock solution contains 1.37 M NaCl, 27 mM KCl, 100 mM Na2 HPO4 , 20 mM KH2 PO4 in distilled water. Adjust pH to 7.4 with HCl if necessary. Autoclave at 120◦ C for 20 min before storage at rt. Working buffer is prepared by diluting one part of the stock solution with nine parts of distilled water. 2. CTC solution: dissolve 6 mg CTC (Sigma) in 1 mL distilled water. Sterilize by filtration. Working solution is prepared by diluting the stock solution 1:4 in sterile 1 × PBS to obtain a 5 mM CTC solution. 3. DAPI solution: dissolve 10 mg DAPI (Sigma) in 1 mL distilled water. Sterilize by filtration. Working solution is prepared by diluting the stock solution 1:1,000 in sterile 1 × PBS to obtain a 10 ␮g/mL DAPI solution. 4. FITC solution: dissolve 10 mg FITC (Sigma) in 1 mL acetone. Sterilize by filtration. Dilute the stock solution to 6 ␮g/mL in sterile NaPB (see Note 3).

2.1.4. Mowiol-DABCO Antifade-Mounting Medium

1. In a 50 mL Falcon tube, mix 6 mL glycerol (Sigma), 2.4 g mowiol 4-88 (Fluka, Buchs, Switzerland), and 6 mL of distilled water. 2. Vortex well and shake at rt for 2 h to dissolve mowiol. 3. Add 12 mL of 0.2 M Tris–HCl, pH 8.5, and incubate at 50◦ C with occasional mixing until the mowiol dissolves (this will take approximately 3 h). 4. Filter through 0.45 ␮m filters and store aliquots of 100–500 ␮L in glass vials at –20◦ C (see Note 4). 5. On the day of use, add 0.6% (w/v) 1,4-diazobicyclo-(2, 2, 2)-octane (DABCO) and vortex for about 30 min (see Note 5).

2.2. Scanning Electron Microscopy 2.2.1. Bacterial Culture and Poly(l-lysine)Coated Cover Glasses 2.2.2. Fixative Solutions

(See Sections 2.1.1 and 2.1.2)

1. 100 mM potassium phosphate buffer, pH 7.4 (KPB): stock solution is prepared by mixing 80.2 mL of 1 M K2 HPO4 and 19.8 mL of 1 M KH2 PO4 while stirring. Both monobasic and dibasic potassium phosphates are dissolved in distilled water. Sterilize by filtration (0.45-␮m filters). 2. 2.5% (v/v) glutaraldehyde solution in KPB (see Note 6).


2.2.3. Dehydration

2.2.4. Critical Point Dryer (e.g., Critical Point Dryer CPD020 from Bal-Tec, Balzers, Liechtenstein) 2.2.5. Gold Coating

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1. Graded ethanol solution series: prepare 30, 50, 70, 80, 96, 100% (v/v) ethanol solutions in distilled water.

2.2.5. Sample Mounting 1. Leit-C conducting carbon cement (Agar Scientific, Stansted, UK) (see Note 7). 2. SEM Pin Stubs. 1. Sputter coater device (e.g., Sputter SCD 040, Bal-Tec, Balzers, Liechtenstein).

2.3. Transmission Electron Microscopy 2.3.1. Bacterial Culture and Poly(l-lysine)-Coated Cover Glasses

2.3.2. Buffers and Fixative Solutions

(See Sections 2.1.1 and 2.1.2)

1. 0.1 M cacodylate buffer, pH 7.4 (CB): dissolve 2.14 g of sodium cacodylate trihydrate (Na(CH3 )2 AsO2 3H2 0) in approximately 60 mL of distilled water. Adjust the pH to 7.4 with 0.1 M HCl (approximately 2.7 mL), then add distilled water up to a final volume of 100 mL (see Note 8). 2. 2.5% (v/v) glutaraldehyde solution in CB: add 1 mL of 25% glutaraldehyde stock solution to 9 mL of CB. Preferably use fresh solutions (see Note 6). 3. 1% (v/v) osmium tetroxide in CB: clean a glass ampoule containing 0.1 g osmium tetroxide, then score it with diamond pencil, and place it in a dark glass bottle. Break the ampoule by vigorously shaking the bottle and add 10 mL of CB. Leave at rt, in the dark, for at least 24 h for a complete dissolution and finally filter the fixative solution with filter paper to eliminate glass fragments deriving from ampoule breakage (see Note 9).

2.3.3. Dehydration and Resin Embedding

1. Graded ethanol solution series: prepare 30, 50, 70, 96, and 100% (v/v) ethanol solutions in distilled water. 2. Propylene oxide (1,2-epoxypropane) (see Note 10). R 3. Durcupan ACM Fluka, epoxy resin (Fluka): the embedding medium is prepared by combining four different components in the following proportions: component A, M (epoxy resin), 30 mL; component B (hardener 964), 30 mL; component C (accelerator 960), 1.2 mL; component D (containing plasticizer), 0.6 mL. Pour into a disposable beaker, mix thoroughly with a glass rod, then with a

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magnetic stirrer. The resulting embedding mixture can be stored in a refrigerator for short periods, if tightly sealed (see Note 11). 2.3.4. Semi-thin and Ultrathin Section Staining

1. 1% (w/v) toluidine blue in 1% (w/v) borax solution: dissolve 1 g of borax (sodium tetraborate) in 100 mL of distilled water, then add 1 g of toluidine blue. Filter with filter paper and store at rt. 2. 5% (w/v) uranyl acetate in 70% (v/v) ethanol: dissolve 0.25 g of uranyl acetate in 5 mL of 70% (v/v) ethanol in distilled water. Filter before usage and keep the solution in the dark (see Note 12). 3. Reynold’s lead citrate: mix 1.33 g of lead nitrate (Pb(NO3 )2 ) and 1.76 g of trisodium citrate (Na3 (C6 H5 O7 ). 2H2 O) with 30 mL distilled water (freshly prepared and carbonate-free) in a stoppered volumetric flask, inverting at intervals of about 10 min. Leave it standing for 30 min, then add 8 mL of 1 N NaOH and distilled water (both freshly prepared and carbonate-free) up to a final volume of 50 mL. Mix again, by inversion, until the solution becomes clear. The final pH should be about 12. Store at 4◦ C (see Note 13).

2.3.5. Negative Staining

1. 2% (w/v) phosphotungstic acid solution in water. Add 0.1 g of sodium phosphotungstate powder (PTA, Fluka) to 10 mL of distilled water in a well-cleaned glass vial. Adjust the pH to 7.2–7.4 with 0.1 N NaOH (see Note 14). 2. Carbon–formvar-coated EM grids (300–400 mesh).

3. Methods 3.1. Fluorescence Microscopy

3.1.1. Bacterial Culture

Combining fluorescence and transmitted light signal is a particularly powerful technique for illustrating details of a cell layer that may not be fully fluorescent. The choice of labels depends upon the availability of filters and fluorochromes. 1. Bacteria are inoculated in 10 mL LB broth and grown at 37◦ C (use an incubator with shaking at 150 rpm), until an OD590 0.8 is reached. 2. Bacteria are harvested by centrifugation, washed twice in NaPB, and resuspended in the same buffer. 3. Approximately 2 × 107 cells (in 50 ␮L) are transferred into a 1.5-mL eppendorf tube, where the peptide is added at the desired concentration. A control sample, without peptide, is also included.


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4. Samples are incubated in a thermomixer, with shaking at 600 rpm, at 37◦ C for 15 min. 3.1.2. Preparation of Poly(l-lysine)-Coated Cover Glasses

1. Clean cover glasses by immersion in alkaline wash solution for at least 2 h. For this purpose, cover glasses are picked up one by one with tweezers and placed into a plastic petri dish filled with the alkaline solution. 2. Remove the alkaline solution with a pipette and rinse glasses five times with distilled water. 3. Remove water and add pure ethanol. 4. Leave cover glasses immersed for 30 min (see Note 15). 5. Take out each single cover glass with sterile tweezers and flame it quickly (see Note 16). 6. Transfer each sterile cover glass into a well of a 24-wells polystyrene plate. 7. Coat each glass with 1 mL of the poly(L-lysine) solution. 8. Incubate at rt for 2 h. 9. Remove the poly(L-lysine) solution with a pipette and wash glasses with sterile water. 10. Let cover glasses drying at rt for at least 3 days before usage (see Note 17).

3.1.3. Preparation of Samples for Triple-Staining (CTC–DAPI–FITC)

1. After peptide treatment, 900 ␮L of CTC (5 mM in PBS 1X) are added to each eppendorf tube. 2. Incubate samples in a thermomixer, at 37◦ C for 90 min, with agitation (150 rpm). 3. Pour the cell suspension of each sample onto a poly (L-lysine)-coated cover glass, previously placed in the well of a 24-wells polystyrene plate. 4. Incubate the plate at 30◦ C for 45 min to allow the adhesion of bacteria. 5. Withdraw the CTC solution and wash with 800 ␮L of NaPB to remove non-attached cells. 6. Repeat washing four times (see Note 18). 7. Add 1 mL of DAPI solution (10 ␮g/mL in PBS) to each well and incubate for 30 min at 30◦ C. 8. Remove DAPI solution and rinse cover glasses with 800 ␮L of NaPB. Repeat washing three times. 9. Add 1 mL of FITC solution (6 ␮g/mL in NaPB) to each well. 10. Incubate the plate at 30◦ C for 30 min. 11. Withdraw the FITC solution and rinse cover glasses with 800 ␮L of NaPB. 12. Repeat washing four times.

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3.1.4. Sample Mounting

1. With a Pasteur pipette, put 1 or 2 drops of antifademounting medium on a microscope glass slide. 2. Place the cover glass (upside down) over the mounting medium. 3. Dry slides horizontally at rt overnight, well covered. 4. Observe the sample with a fluorescence microscope. Excitation at 359 nm induces DAPI fluorescence (blue emission, 461 nm); excitation at 490 nm induces FITC fluorescence (green emission, 520 nm); excitation at 450 nm induces CTC–formazan fluorescence (red emission, 630 nm). Examples are shown in Fig. 16.1.

Fig. 16.1. Detection of total, viable, and membrane-perturbed bacteria using triple staining with fluorescent probes. E. coli cells were grown and treated with temporin L at sub-lethal (2 ␮M) and lethal (50 ␮M) concentrations. Bacteria were then immobilized on poly(L-lysine)-coated glass slides and incubated with CTC, DAPI and FITC as described in the protocol. Panels (a), (b), and (c) illustrate staining with DAPI, FITC, and CTC, respectively. (Reproduced with permission, from Mangoni et al. (7). © the Biochemical Society.).


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3.2. Electron Microscopy

For electron microscopy, samples must be completely dry, because both SEM and TEM work in vacuum. However, to avoid disruption of biological samples, as a result of the loss of their own water, you can preserve and stabilize the sample’s structure by using different fixatives that cross-link molecules and trap them together as a stable structure. After fixation, samples are dried in graded ethanol solution series. In the case of SEM, this procedure is followed by a physical (critical point drying, CPD) (see Note 19) or chemical dehydration process (see Note 20).

3.2.1. Scanning Electron Microscopy

In the case of SEM, dehydrated samples must be electrically conductive. For this purpose, they are coated with a thin film of electrically conductive material, usually gold.

3.2.1.1. Adhesion of Bacteria to Poly(l-lysine)-Coated Cover Glasses

1. Exponentially growing bacteria in LB medium (see Section 3.1.1) are harvested by centrifugation, washed twice in NaPB, and resuspended in the same buffer. Approximately 2 × 107 cells (in 50 ␮L) are transferred into a 1.5-mL eppendorf tube and the peptide is added at the desired concentration. 2. After peptide treatment, add 150 ␮L of NaPB and pour the bacterial suspension on a poly(L-lysine)-coated cover glass, previously placed in a well of a 24-wells polystyrene plate. 3. Incubate the plate for 90 min at 30◦ C to allow the adhesion of bacteria. 4. Wash each cover glass with 800 ␮L of NaPB to remove nonadherent bacteria. Repeat washing four times (see Note 21).

3.2.1.2. Fixation

1. Withdraw NaPB and add 800 ␮L of 2.5% glutaraldehyde solution to each well. 2. Incubate the plate for 2 h at 4◦ C. 3. Remove the glutaraldehyde solution. 4. Rinse cover glasses with 1 mL KPB (kept at 4◦ C). 5. Leave the plate at 4◦ C for 10 min. 6. Remove buffer. 7. Repeat Steps 4–6 three times

3.2.1.3. Dehydration

1. Add 1 mL of 30% ethanol to each well, incubate at rt for 2 min, and remove the alcohol. Repeat twice. 2. Add 1 mL of 50% ethanol to each well, incubate at rt for 2 min, and then remove the alcohol. Repeat twice. 3. Add 1 mL of 70% ethanol to each well, incubate at rt for 2 min, and then remove the alcohol. Repeat twice.

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4. Add 1 mL of 80% ethanol to each well, incubate at rt for 5 min, and then remove the alcohol. Repeat twice. 5. Add 1 mL of 96% ethanol to each well, incubate at rt for 5 min, and then remove the alcohol. Repeat twice. 6. Add 1 mL of pure (100%) ethanol to each well, incubate at rt for 5 min, and then remove the alcohol. 7. Repeat twice and leave cover glasses in 2 mL of 100% ethanol (see Note 22). 3.2.1.4. Critical Point Drying

1. Put a small envelope made of optical paper (see Note 23) in a petri dish filled with pure ethanol. If more than one sample has to be dried at the same time, label the envelope outside with a pencil (see Note 24). 2. Insert each single cover glass coated with bacteria into the paper envelope. 3. Close the envelope with a stapler. 4. Transfer samples into the chamber of the CPD device (see Note 25). 5. Process for CPD following manufacturer’s instructions.

3.2.1.5. Mounting

1. Remove samples from CPD device. 2. Open the paper envelope with the help of tweezers and remove each cover glass. 3. By using a toothpick, apply a very thin layer of conductive glue on the stubs. 4. Mount each cover glass on the stub (see Note 26). 5. Wait for the glue to dry.

3.2.1.6. Gold Coating and Sample Observation

1. Insert mounted samples on a sputter coater device. 2. Select sputter parameters to obtain a conductive film of about 15 nm. 3. View sample under SEM. An example is given in Fig. 16.2.

3.2.2. Transmission Electron Microscopy

With regard to TEM, the sample has to be of such a low density to permit electrons (that have relatively low penetrating power) to travel through it. The two most frequently employed procedures to prepare biological samples for TEM observation are resin embedding and ultrathin sectioning and negative staining. For resin embedding and ultrathin sectioning, after fixation and dehydration, the sample is embedded in a plastic resin that subsequently polymerizes into a solid hard plastic block. The block is cut into ultrathin sections (50–100 nm thick) that are placed on a metal grid and then stained with heavy metal salts.


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Fig. 16.2. SEM observation of E. coli cells before and after 15 min treatment with temporin L, at a lethal concentration (50 ␮M). Each figure has been magnified × 15,000 or × 30,000. (Reproduced with permission, from Mangoni et al. (7). © the Biochemical Society.).

These compounds can react with various molecular components of the cell and, because of the good capacity to scatter electrons of their metal atoms, significantly improve the image contrast in the microscope. By following this procedure, in-depth ultrastructural analysis of the sample can be performed. In the case of negative staining, this faster and less expensive method is suitable for imaging suspensions of small and particulate samples (e.g., bacteria, viruses, cell components and purified macromolecules). The sample is spread onto a grid coated with a plastic-support film and mixed with a “negative stain” solution (phosphotungstic acid/neutralized potassium phosphotungstate, ammonium molybdate, or uranyl acetate). Importantly, an advantage of this method is that, beside providing contrast between specimen and background, the layer of negative stain preserves the macromolecular structure of the sample and protects it from the collapse due to the dehydration process as well as from irradiation damage. 3.2.2.1. Preparation of Resin-Embedded Samples (Cell Processing, Fixation, Dehydration, and Resin Embedding)

1. Exponentially growing bacteria in LB medium (see Section 3.1.1) are harvested by centrifugation, washed twice in NaPB, and resuspended in the same buffer. Approximately 2 × 107 cells are transferred into a 1.5-mL eppendorf tube where the peptide is then added. 2. After peptide treatment, centrifuge bacteria at 300×g for 20 min. 3. Wash twice with NaPB, then remove NaPB, and replace it with 2.5% glutaraldehyde in CB. Resuspend the cells in the fixative solution and keep the sample at 4◦ C for 1 h.

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4. Spin the bacterial suspension at 13,500×g in 0.3 mL polypropylene microcentrifuge tubes (with a microcentrifuge) for 15 min at 4◦ C. Discard supernatant by inverting the tube and remove the resulting pellets by cutting off the bottom end of the tubes with a clean razor blade and place them into small glass beakers (see Note 27). 5. Wash the pellets in CB (5 times × 10 min). 6. Post-fix with 1% (v/v) osmium tetroxide in CB for 1 h at 4◦ C. 7. Rinse twice with CB for 5 min. 8. Dehydrate samples through ascending ethanol solution series: 30, 50, 70, and 96% ethanol, for 5 min each at 4◦ C, then pure (100%) ethanol for 15 min at 4◦ C, and finally pure ethanol for 15 min at rt. 9. Replace ethanol with propylene oxide (3 times × 20 min). R ACM 10. Replace propylene oxide with Durcupan resin/propylene oxide mixture, 1:1 (v/v). To facilitate resin infiltration into the samples, place the beakers on a slow turning wheel device: the slow rotatory movement will provide the necessary mixing during incubation. Leave for 1 h at rt, under a fume hood. Then, replace with fresh resin/propylene oxide mixture, 1:1 (v/v), and leave overnight.

11. Remove 1:1 (v/v) resin/propylene oxide mixture and replace with 3:1 (v/v) resin/propylene oxide mixture (2 × 1 h at rt on the slow turning wheel, under a fume hood). 12. Remove 3:1 (v/v) resin/propylene oxide mixture and replace it with pure resin (2 × 1 h). Put the beakers on the slow turning wheel, in an oven, at 37◦ C. 13. By carefully using a toothpick or a suitable needle, transfer the pellets to fresh resin in molds and leave them in the oven at 37◦ C for 24 h, then at 70◦ C for 72 h, for polymerization. 3.2.2.2. Semi-thin and Ultrathin Section Staining

1. Once the blocks have polymerized, they are removed from the molds and may be appropriately trimmed and used for semi-thin sectioning with an ultramicrotome: semi-thin sections (about 1 ␮m thick) are cut using a glass knife and placed on a drop of water over a glass slide. The glass slide is then put on a hotplate at about 80◦ C to ensure adhesion of the sections to the glass surface upon water evaporation, and these are finally stained with 1% (w/v) toluidine blue in 1% (w/v) borax solution for 1 min at 60◦ C. After rinsing with distilled water and drying, the semi-thin sections can be observed with a light microscope to select a suitable area of the sample for ultrathin sectioning.


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2. After further trimming of the blocks, ultrathin sections (about 50–100 nm thick) are cut and picked up onto electron microscopy copper grids (usually, several sections may be collected on each single grid). 3. For the classic “double staining” method, ultrathin sections are “stained” first with 5% (w/v) uranyl acetate in 70% (v/v) ethanol: place a droplet of the staining solution on a clean piece of parafilm (protected from direct light exposure); put the grid on the droplet, with the sections side down, and leave for 15–25 min at rt. Rinse thoroughly the grid with filtered distilled water. 4. After uranyl acetate, the ultrathin sections are treated with Reynold’s lead citrate. In this case, a droplet of the staining solution is placed in a petri dish containing a few pellets of sodium hydroxide, which has the ability to absorb atmospheric carbon dioxide, thus protecting the lead acetate solution and avoiding lead carbonate precipitation and section contamination. Again, the grid is placed, with the sections side down, on the droplet of staining solution and left for 15–25 min at rt, before rinsing thoroughly with filtered, carbonate-free distilled water. 5. After staining and washing, the grids are allowed to dry in a desiccator before TEM observation. 3.2.2.3. Negative Staining (Drop Method)

1. Exponentially growing bacteria in LB medium (see Section 3.1.1) are harvested by centrifugation, washed twice in 10 mM NaPB, and resuspended in the same buffer. Approximately 2 × 107 cells (in 100 ␮L) are transferred into a 1.5-mL eppendorf tube and treated with the peptide. 2. After peptide treatment, centrifuge cells at 300×g for 20 min. 3. Resuspend the pellet in 300 ␮L of NaPB (see Note 28). 4. Place a small droplet of the bacterial suspension onto a formvar-coated grid (see Note 29). 5. After a few seconds (usually 10–30 s should be enough to allow the absorption of bacterial cells to the formvar film), “wash” the grid with about 10 droplets of the negative staining PTA solution (see Note 30). 6. Leave the last drop of PTA solution on the grid for 10 s, then remove the excess of liquid by touching the edge of the grid with a piece of filter paper. 7. Allow the grid to dry in a desiccator, until the following day, before microscopic observation with TEM (see Note 31). An example is given in Fig. 16.3.

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Fig. 16.3. Negative staining of E. coli cells for TEM observation. (a), Intact bacteria; (b), bacteria in the presence of the synthetic antimicrobial peptide K5L7 at the minimum inhibitory concentration (MIC); (c), bacteria in the presence of K5L7 (enlargement); and (d), bacteria in the presence of K5L7 at a concentration of less than MIC. Contributed by Yechiel Shai, Weizmann Institute, Rehovot, Israel.

4. Notes 1. Use heat to solubilize these salts. 2. Be careful when NaOH is dissolved in water, because this is an exergonic reaction, which generates heat. Do not store this solution in glass bottles.


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3. Wrap staining solutions with aluminum foils to protect them from light. 4. Mowiol-mounting medium can be stored at rt not more than 1 month. Before usage, it is recommended to warm it at rt to avoid bubble formation. 5. Fluorescently labeled cells and tissues exhibit a characteristic photobleaching curve in response to excitation. Much of the photobleaching can be attributed to the generation of free radicals. The use of free radical scavengers has been shown to decrease the rate of photobleaching. Common scavengers include n-propyl gallate, p-phenylenediamine, and DABCO, whereas live systems have been reported to reduce photobleaching in the presence of vitamin C. If possible, liquid embedding media should be used; samples mounted in liquid media seem not to shrink in volume over time, when sealed properly, and can be stored at –20◦ C. 6. Handle glutaraldehyde carefully. It is an irritant for skin and mucosa (ocular and first respiratory tracts). Avoid prolonged breathing and contact with eyes. Glutaraldehyde should be used under a fume hood. 7. This is supplied in the form of a suspension of very fine conducting carbon particles in a volatile carrier. Good for forming conducting bonds between specimen and stub. 8. Sodium cacodylate is highly toxic. Always wear gloves and work under a fume hood. 9. Osmium tetroxide is easily reduced by impurities and light exposure. Use only acid-cleaned glassware (thoroughly rinsed in distilled water), store solutions in the dark (at 4◦ C for prolonged periods) but discard if a reddish color develops. When using osmium tetroxide, always wear gloves and work under a fume hood to avoid exposure to its dangerous vapors. 10. Propylene oxide is very reactive, extremely volatile, and carcinogenic, so caution should be observed when using this solvent. Always wear suitable gloves and work under a fume hood. 11. Be careful in handling epoxy resins, since they may cause severe irritation upon prolonged or repeated contact. Wear suitable gloves and work under a fume hood. 12. Uranyl acetate is slightly radioactive and a very toxic substance, with cumulative effects. Follow appropriate precautions to limit exposure to it, wear gloves, and possibly work under a fume hood. 13. Wear gloves when using lead citrate and avoid excessive exposure to this toxic compound. Lead citrate solutions readily absorb carbon dioxide, with formation of a

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precipitate of lead carbonate that may contaminate sections. Care should be taken not to breathe (thus emitting CO2 ) on lead citrate during staining. Reynold’s lead citrate can be kept at 4◦ C for several months if tightly stoppered. Discard it if precipitate appears. 14. PTA is corrosive and causes burns. Negative stains are all heavy metals and should be handled as toxic and hazardous materials (the usage of suitable protective clothes, gloves, eye/interface protection as well as a fume hood is recommended). Note that negative staining does not kill pathogens. Thus, the infectious agent should be inactivated prior to negative staining and the grid should be sterilized by gas or ultraviolet radiation. The negative stain solution can be stored for 1–3 weeks at 4◦ C. 15. To completely remove the alkaline solution, it is important that each cover glass remains separated by the others. This is to avoid the formation of a white mark on the glass after sterilization by flame. 16. Be careful, do not flame cover glass until alcohol is not completely evaporated. 17. To avoid attachment of the cover glass to the plastic, place it on the surface of a 96-wells plate. It is important that both sides of the glass are in contact with air. 18. During washing, make sure to pipette the buffer solution on the wall of the well and not directly on the top of the cover glass. 19. Since air drying of hydrated biological specimens can result in collapse and shrinkage, due to the surface tension between water and vapor, CPD can avoid this problem by placing the specimen in an environment where the fluid, within the specimen, can pass from the liquid to gas phase with zero surface tension. The best transition fluid is represented by carbon dioxide, because its critical point is reached under conditions that do not damage the biological sample (31ºC and 73.8 bar). Once carbon dioxide is fully converted to gas, the specimen is dry. In practice, it is necessary to fix the specimen and then to transfer it into an “intermediate fluid” (typically ethanol, as water is not miscible with CO2 ), according to the scheme below: H2 O (wet specimen)

Ethanol (intermediate fluid)

Liquid CO2

CPD (dry specimen)

20. Chemical dehydration by hexamethyldisilazane (HMDS) can be carried out as a good alternative to CPD. Compared with CPD, HMDS drying takes a shorter time, less effort,


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no equipments, and lower costs (10). The procedure is as follows: (a) after dehydration phase with ethanol, transfer dry cover glasses into the wells of a new 24-wells polystyrene plate; (b) add 1 mL of HMDS (Sigma) in each well. HMDS is toxic and harmful by inhalation; carry out all these steps under a fume hood; (c) incubate the plate at rt for 30 min; (d) remove HMDS with a Pasteur pipette; (e) allow cover glasses to dry until the next day. 21. In this phase of bacteria fixation, cells are still alive. 22. At this point, it is crucial to avoid that cover glasses run dry. 23. Make the envelope by closing (with a stapler) three sides of a folded sheet of optical paper around each cover glass. 24. It is very important not to forget to properly position the cover glass into the envelope: the poly(L-lysine)/bacteria side should be directed toward the labeled side of the envelope. 25. In all these phases, samples must be kept wet. 26. When you put the cover glass on the stub, make sure that the emptied side of the cover glass (without bacteria) is in contact with the glue, otherwise you will loose your sample! 27. After primary aldehyde fixation, bacteria cell pellets should be cohesive enough to be handled during subsequent processing steps, as if they were tissue pieces. If this is difficult to achieve, or if too small pellets are obtained because of the limited number of cells which are present in the sample, the suspensions of glutaraldehyde-fixed cells can be pelleted and embedded in agar. Different methods can be used for this purpose, but the common net result is the formation of agarized cell pellets, sufficiently hard and large for further handling. 28. A good negative staining preparation should ideally produce a single layer of individual, well-separated bacterial cells on the coated grid. If the original suspension is too concentrated, several grids may be prepared from serial dilutions of the sample. 29. Formvar, otherwise known as polyvinyl formal, appears to be the most widely used support film for TEM grids worldwide. During this step, you can keep the grid a bit raised from the bench by using tweezers. 30. Negative stains do not interact with biological samples; they rather adsorb to the specimen particles and, upon drying, enclose them forming a structureless, smooth glassy matrix that surrounds external/accessible internal surfaces

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of each particle and penetrate, to a certain extent, into their irregularities. 31. Typically, stain clouds or “shadows” are obtained around small portions of the sample, producing a strong contrast with respect to the background. This is because of the different electron density (i.e., electron scattering power) between the organic matter and the surrounding metal atoms. As a consequence, the sample will appear as a negative picture (light areas on a dark background) when observed under TEM, and its morphology and fine structural details will be clearly distinguishable (see Fig. 16.3).

Acknowledgments We thank Prof. Donatella Barra for careful reading the manuscript. Work reported here has been supported in part by grants from the Italian Ministry of Education, University and Research and from the Università di Roma “La Sapienza”. References 1. Boman, H. G. (1995) Peptide antibiotics and their role in innate immunity. Annu. Rev. Immunol. 13, 61–92. 2. Hancock, R. E. and Sahl, H. G. (2006) Antimicrobial and host-defense peptides as new anti-infective therapeutic strategies. Nat. Biotechnol. 24, 1551–1557. 3. Zasloff, M. (2002) Antimicrobial peptides of multicellular organisms. Nature 415, 389–395. 4. Jenssen, H., Hamill, P., and Hancock, R. E. (2006) Peptide antimicrobial agents. Clin. Microbiol. Rev. 19, 491–511. 5. Nicolas, P. and Mor, A. (1995) Peptides as weapons against microorganisms in the chemical defense system of vertebrates. Annu. Rev. Microbiol. 49, 277–304. 6. Mookherjee, N. and Hancock, R. E. (2007) Cationic host defence peptides: innate immune regulatory peptides as a novel

7.

8.

9. 10.

approach for treating infections. Cell. Mol. Life Sci. 64, 922–933. Mangoni, M. L., Papo, N., Barra, D., Simmaco, M., Bozzi, A., Di Giulio, A., and Rinaldi, A. C. (2004) Effects of the antimicrobial peptide temporin L on cell morphology, membrane permeability and viability of Escherichia coli. Biochem. J. 380, 859–865. Rodriguez, G. G., Phipps, D., Ishiguro, K., and Ridgway, H. F. (1992) Use of a fluorescent redox probe for direct visualization of actively respiring bacteria. Appl. Environ. Microbiol. 58, 1801–1808. Severin, E., Stellmach, J., and Nachtigall, H. M. (1985) Fluorimetric assay of redox activity in cells. Anal. Chim. Acta 170, 341–346. Nation, J. L. (1983) A new method using hexamethyldisilazane for preparation of soft insect tissues for scanning electron microscopy. Stain Technol. 58, 347–351.

Chapter 17 Molecular Simulations of Antimicrobial Peptides Allison Langham and Yiannis N. Kaznessis Abstract Recent advances in molecular dynamics (MD) simulation methods and in available computational resources have allowed for more reliable simulations of biological phenomena. From all-atom MD simulations, we are now able to visualize in detail the interactions between antimicrobial peptides (AMPs) and a variety of membrane mimics. This helps us to understand the molecular mechanisms of antimicrobial activity and toxicity. This chapter describes how to set up and conduct molecular dynamics simulations of AMPs and membrane mimics. Details are given for the construction of systems of interest for studying AMPs, which can include simulations of peptides in water, micelles, or lipid bilayers. Explanations of the parameters needed for running a simulation are provided as well. Key words: Molecular dynamics, CHARMM, NAMD, micelles, lipid bilayers.

1. Introduction 1.1. Why Computer Simulations?

Molecular dynamics (MD) simulations can provide some of the molecular level details necessary to understand the mechanism of action of antimicrobial peptides (AMPs). For many AMPs, it is apparent that the cell membrane is the target. The general interaction between positively charged AMPs and negatively charged bacterial membranes is well understood, as it is the need for hydrophobic content to allow for interactions between the peptide and the membrane core. However, these basic facts are not enough to allow for design of AMPs of therapeutic value. There is no simple, linear correlation between peptide charge or hydrophobicity and antimicrobial activity. Consequently, intuitive design rules for novel AMPs are hard to deduce. The wide variety of sequences and structures of naturally occurring AMPs suggests


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that there is most certainly not one mechanism of action by which all peptides act. In this chapter, we discuss the use of MD simulations to study AMPs. The goals in using MD simulations are to both understand the mechanism of action by which these peptides kill bacteria and develop predictive models that can be used to design highly potent, yet non-toxic peptides. We should note that computer simulations have as steep a learning curve as any sophisticated experimental method. The logistics of running computer simulations can also be challenging, from setting up the system, to choosing numerical integration schemes and statistical ensembles, to managing and analyzing large volumes of data. Nonetheless, as with any sophisticated experimental method, the pleasure of discovery awaits on the other side of a tortuous effort. 1.2. Theory

For a thorough review of the underlying theory of MD simulations, the reader is directed to Allen and Tildesley’s “Computer Simulation of Liquids” (1). MD simulations are based on classical mechanics or, more specifically, on Newton’s second equation of motion. If the force acting on each atom in a system is known, the acceleration can be determined. Using this acceleration, the equations of motion can be integrated, resulting in a trajectory of the positions, velocities, and accelerations of each particle in the system. The force Fi on an atom of mass mi , which is at position ri , is determined from the potential energy of the system, V, as shown in equation [1]. The potential can be used to directly determine the position of a particle as a function of time, as in equation [2]. F = −∇V

[1]

d2 r i dV = mi 2 dri dt

[2]

The equations of motion are solved for each atom in the system. The forces acting on the atoms in the new positions are calculated and the simulation continues for as many time steps as necessary. Empirical energy functions are used to approximate the force fields for large biological systems composed of many atoms. Some common force fields are AMBER (2), OPLS/AMBER (3), CHARMM (4), and GROMOS (5). We focus here on the CHARMM (Chemistry at HARvard Macromolecular Mechanics) force field, which has been developed over the last 25 years, and is continuously revised to better match new experimental data. There are also several commercially available MD simulation engines for use empowered with the above force fields. We

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recommend the use of the CHARMM MD simulation engine or NAMD (NAnoscale Molecular Dynamics) (6). A number of CHARMM scripts for the design and analysis of a variety of simulation systems are available on the CHARMM forum (www.charmm.org). However, NAMD is designed to take advantage of advances in parallel computing. This permits longer simulations of larger systems than are possible with CHARMM. We should note that more recently a graphics user interface has been developed for CHARMM that significantly simplifies the set up of simulation systems and parameters. The software is available at http://www.charmm-gui.org/. 1.2.1. The Potential Function

The potential function is a sum of interaction energies. The value of the potential is determined by summing the bonded terms with the non-bonded potential terms, Vbonded and Vnon-bonded , respectively: V (R) = Vbonded + Vnon-bonded

1.2.1.1. Non-bonded Terms

[3]

The non-bonded energy terms account for interactions between non-bonded atoms and atoms that are more than three covalent bonds away from each other in a molecule. These are modeled by the van der Waals energy and electrostatic energy, the first and second summation terms in equation [4], respectively.

Vnon-bonded =

4ε

non-bonded pairs

+

non-bonded pairs

σik rik

12 6 – σrikik [4]

qi q j Dri j

The calculation of the non-bonded terms in the potential function is the most time-consuming part of the MD simulation. In principle, the interactions between every pair of atoms should be calculated explicitly, meaning that for an N-atom system, N2 calculations would be required. To decrease this number, methods were developed to ignore the interactions between two atoms separated by a distance greater than a specified cutoff distance. For the van der Waals interactions, the potential is “shifted” off over a period ron to roff : Atoms farther from each other than the distance roff are assumed not to interact. For the electrostatic interactions, cutoff schemes have been shown to be inaccurate when computing electrostatic interactions (7). Instead, the Ewald summation is used, which separates the potential into a slowly decaying long-range component and also a quickly varying short-range component. There are several parameters that need to be optimized when solving the Ewald

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summation. For large systems, it is best to fix the real sum cut off, R cutoff , and choose a value for the width of the Gaussians, α, that is large enough to accelerate convergence of the real sum. The value of α determines the relative rate of convergence of the real and reciprocal sums. The accuracy of the sum is independent of α. In practice, when the Ewald sum is used, the Gaussian source distributions centered on point ions are sampled onto a finite grid and the resulting Fourier integral is approximated by a Fourier series, which is evaluated numerically using Fast Fourier Transforms. Complex exponentials in the reciprocal sum are evaluated by ␤-spline interpolation. Therefore, the grid point spacing and the ␤-spline order must be optimized. The grid point spacing dictates the number of grids in each direction in the simulation cell onto which the Gaussian charges are interpolated. The ␤-spline is used to interpolate charges onto the grids. Higher values give more accurate sums but at a greater computational cost. In order for Ewald’s method to be appropriately applied to a simulation, the system must have no net charge. 1.2.1.2. Bonded Terms

The bonded terms include the bonds, angles, and bond rotations in the molecule (Fig. 17.1) and are computed using equation [5]: Vbonded =

K b (b − b0 )2 +

pairs

+

K θ (θ − θ0 )2

angles

K φ (1 − cos(nφ))

[5]

dihedral pairs

Fig. 17.1. Bonded interaction motions: (a) bond stretch is the movement between atoms directly bound to each other; (b) angle bend is a function of the relative position of atoms separated by one additional atom (1–3 pairs); (c) rotatealong-bond (dihedrals) is a function of the relative position of atoms separated by two additional atoms (1–4 pairs).

These terms are calculated using approximations for each type of motion. The bond-stretch term is a harmonic potential approximated as a function of displacement from the ideal bond length, b 0 for 1,2-pairs of atoms. The force constant, Kb , determines the strength of the bond and is determined by the atoms involved in the bond. The angle-bend term is associated with the movement a bond angle, θ, from its ideal value θ 0 and is also represented by a harmonic potential with a force constant, Kθ, which


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depends on the atoms involved. The rotate-along-bond energy is associated with the torsion angle potential function, which takes into account the steric barriers between 1,4-pairs of atoms (atoms separated by three covalent bonds). This potential expressed as a cosine function. 1.2.1.3. Additional Potentials

There are two additional potential terms in the CHARMM force field. The improper dihedrals term (equation [6]) accounts for out of plane bending, where kω is the force constant and ω–ωo is the out of plane angle. The other component is the Urey–Bradley potential (equation [7]), which accounts for angle bending using 1,3 non-bonded interactions. In this term, kU is the respective force constant and u–uo is the distance between the 1,3 atoms in the harmonic potential: E impropers =

E Urey−Bradley =

K ω (ω − ω0 )2

K u (u − u 0 )2

[6] [7]

The CHARMM parameter file contains the parameters for each atom type and bond type. It provides the equilibrium bond lengths and van der Waals radii. 1.2.2. Integration Algorithms

Because there are so many atoms in a MD simulation system and because the energy function is semi-empirical, there is no analytical solution to the equations they formulate. There are many possible integration algorithms. Most are based on Taylor series expansions of the particle position and its derivatives. In CHARMM, the “leapfrog” Verlet algorithm is used. The equations solved in this algorithm are 1 r (t + δt) = r (t) + v t + δt δt 2 1 1 v t + δt = v t + δt + a(t)δt 2 2

[8] [9]

The velocities are calculated at time t + 1/2 δt. These velocities are then used to calculate positions r at the time t + δt, so that the velocities “leap” over the positions, then the positions “leap” over the velocities (1). In NAMD, the velocity Verlet algorithm is used. In this method, which minimizes round-off error, the positions, velocities, and accelerations are stored at time t(1). The equations used are r (t + δt) = r (t) + δtv(t) +

1 2 δt a(t) 2

[10]

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1 1 v t + δt = v(t) + δt[a(t) + a(t + δt)] 2 2

[11]

The time step, δt, used with these algorithms is of importance. A smaller time step means slower dynamics. On the other hand, a large time step can cause instability due to large jumps in the conformation negatively impacting the energy of the system. The time step must be much smaller than the fastest characteristic motion within the system. For biological systems, this motion is usually the vibration of hydrogen bonds. A time step of 2 fs (2 × 10–15 s) has been used widely for biological molecules when the SHAKE algorithm is employed to constrain the hydrogen bonds. 1.3. Temperature and Pressure Control

One can show that simply solving Newton’s equations of motion for a system of N particles in volume V conserves the total energy of the system. Indeed any classical mechanical set of equation of motion samples the microcanonical, or NVE ensemble, where N, V, and E are constant. It is more sensible to simulate biological systems under constant pressure and temperature constraints. The equations of motion need to then be modified appropriately. Temperature is often controlled by using Nose–Hoover–Langevin dynamics. In Langevin dynamics, a stochastic force term is included to introduce the effects of random interactions such as friction between molecules and an occasional high-velocity collision to mimic perturbations that would occur in an experimental system. For constant pressure and temperature simulations in which Langevin dynamics are used to control the temperature, the pressure can be controlled in NAMD with a modified Nose–Hoover method. This method is a combination of the methods described in (8) and (9). The revised equations of motion for this method are given below (equations [12], [13], [14], [15], [16], [17], and [18]), where W is the mass of the piston, τ is the oscillation period, R is the noise on the atoms, and Re is the noise on the piston (10): r = p/m + er

[12]

p = F − e p − gp + R

[13]

V = 3V e

[14]

e = 3 V /W (P − P0 ) − ge e + Re /W

[15]

W = 3 N τ 2 kT

[16]

R 2 = 2mgkT / h

[17]

Re2 = 2W ge kT / h

[18]


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1.4. Atomistic Versus Coarse-Grained Simulations

The previous discussion assumes the implementation of fully atomistic simulations. This is the preferred method for the study of antimicrobial peptides, as the ability of the force fields to reproduce structural and conformational changes diminishes with coarse-grained force fields. However, coarse-grained simulations offer a computationally cheaper approach. In these simulations, the atoms are not represented individually, but are grouped into “pseudo-atoms.” This reduction of the system can allow for the simulation of larger systems or for longer timescales. The level to which the system is reduced can be from the simplest united-atom model, in which the two hydrogens of a methylene group are represented together with the carbon, to groupings of pseudo-atom “beads” that represent two to four methylene groups. As with all-atom simulations, the parameterization for the interactions between beads is empirical. At higher levels of coarse graining, the accuracy of the system behavior is less reliable. For example, simulation of pore formation by the frog AMP magainin has been carried out with a coarse-grained method (11). Simulations of this type might be useful in some applications, but are not the focus of this chapter.

1.5. Implicit Solvation

Implicit solvation (or continuum solvation) is another method for simplifying a fully atomistic simulation. Instead of using fully atomistic “explicit” water molecules, the solvent is represented as a continuous medium, wherein a mean field approach can be used to approximate the behavior of individual solvent molecules. Two common methods use the Poisson–Boltzmann equation or the Generalized Born model. For a more thorough review of the different implicit solvation models, the reader is referred to (12). The Poisson–Boltzmann equation models the electrostatic environment of a solute as a polarizable continuum. In order to further reduce computational expense, more approximations are usually made. For instance, the Generalized Born model is an approximation to the linearized Poisson–Boltzmann equation (13). It is based on modeling the solute as a sphere with different internal dielectric constant than the solvent. Any type of implicit solvation can be used to reduce the number of atoms in the system, but results in the loss of data for the movement of the individual ions and solvent molecules in the system.

1.6. Common Simulation Systems

It has been proposed that AMPs act to kill bacteria through a series of steps: attraction, aggregation, penetration, and lysis (14). Simulations of this process would provide the ultimate level of detail in understanding the mechanism of action of AMPs; however, the timescales on which these processes occur exceed what

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is currently possible with all-atom MD simulations. Formation of pores has been observed in coarse-grained MD simulations (15, 16), but such simulations do not provide the same resolution as atomistic approaches, and may not accurately reflect system properties and behavior. To accommodate the current limitations on computational power, we can explore various steps of this process individually (Fig. 17.2)

Fig. 17.2. The three types of systems typically investigated. Peptide in water (with ions) is shown in (a). This type of simulation can be completed in days. View (b) shows a typical peptide–micelle simulation. A typical micelle simulation can be completed in a span of several weeks. A lipid bilayer is shown in (c). With current computational resources, a lipid bilayer simulation takes several months to complete.

1.6.1. Simulations in Water

One of the simplest systems used in MD of AMPs consists of peptides in water. The simulation box is composed of a single peptide, water, counterions (if necessary to achieve charge neutrality), and additional salt if desired. This can be done simply to study the conformational motions of the peptide, or to measure physicochemical properties that might be related to the activity or toxicity of the peptide. When a set of data is available for a large number of related peptides, predictive quantitative structure–activity relationships (QSARs) can be developed. This is an approach widely used in computer-aided drug design (as described in 17 and demonstrated in 18–23). QSARs, obtained through multiple linear regression, correlate properties calculated from the peptide–water simulations to toxicity of the peptide. The hypothesis is that the properties of monomeric peptides can be related to their hemolytic activity and cytotoxicity. Simulations in water require significantly less computational resources than AMPs in environments mimicking lipid membrane, but can nevertheless provide meaningful results.

1.6.2. Simulations in Micelles

Simulations in water can provide a method for rapid screening of new sequences based on properties of single peptides, but in order to obtain information as to how the peptides interact with


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membrane mimics, and to elucidate the structural or sequence basis for the varying levels of toxicity in several peptide analogues, their interactions with membrane-mimicking micelles can be observed. There are several reasons to use micelles as membrane mimics. Like the lipid bilayers of real membranes, micelles possess a well-defined hydrophobic core and a flexible, hydrophilic interface and are commonly used in place of monolayers or bilayers in experimental methods such as NMR spectroscopy (24–27). Simulations in micelles are much less time and resource consuming than simulations in lipid bilayers, due to their smaller size and faster relaxation times, which have been shown through both direct experiments and simulations to be on the order of 500– 1,000 ps for micelles (28–32), in contrast with lipid bilayers, which require tens of nanoseconds (33, 34). Molecular dynamics studies of micelles have been performed for many types of micelles, including anionic micelles such as those formed by sodium dodecyl sulfate (SDS) (29, 35–38); zwitterionic micelles (e.g., dodecylphosphocholine, DPC) (30, 31, 39–41); and a few mixed composition micelles (42, 43). DPC micelles are considered to be acceptable models of eukaryotic cell membranes, which are generally rich in zwitterionic phospholipids. SDS has been used as a mimic for the negatively charged molecules found in bacterial membranes, because SDS micelles possess an anionic exterior and a hydrophobic interior. The differences of peptide behavior between the SDS micelle and the DPC micelle provide a basis for the study of the activity and toxicity of selected AMPs. Indeed, it is quite possible that AMPs work through different mechanisms to kill bacterial or mammalian cells. In the case of the unstructured indolicidin, for example, the peptide takes on different conformations when interacting with the two types of micelles (44). 1.6.3. Simulations in Lipid Bilayers

The long timescales on which aggregation and penetration of the bilayer by AMPs occur have prohibited the use of fully atomistic MD simulations to study these phenomena. The computational power needed to observe such phenomena using fully atomistic simulations is currently not available. It is possible, however, to study systems for which an initial orientation has been suggested from experimental data. For example, the pore structure of protegrin-1 in a mixed phosphatidylethanolamine (POPE): phosphatidylglycerol (POPG) bilayer was determined from NMR experiments. This was used as a starting configuration for MD simulations of the pore system, allowing a molecular level view of the interactions between the pore and the bilayer system, while eliminating the problems associated with initialization of the system (45).

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2. Materials 1. PDB (Protein Data Bank, http://www.rcsb.org) file for AMP of interest with atomic coordinates. 2. Coordinate files for micelles or lipids, as needed. 3. Visualization software, such as VMD or Rasmol. 4. CHARMM topology and parameter sets (available for free download at http://www.cems.umn.edu/research/ kaznessis/antimicrobial.htm.) 5. Simulation engine (NAMD or CHARMM recommended). 6. Access to supercomputers or UNIX machines.

3. Methods 3.1. System Construction

1. The initial configuration of the peptide should be based on an experimentally determined structure (e.g., through Xray crystallography or NMR), since simulations are not at the point to be able to properly fold a peptide in a reasonable amount of time. The initial peptide coordinate file can be obtained from the Protein Data Bank for many AMPs. The type of simulation will dictate the next steps of system construction. 2. For simulations carried out in water, typically a large box of water is first constructed. This is often done in CHARMM by copying and translating a box of water. Two pre-made boxes of TIP3P water molecules are available, one containing 125 molecules and the other 216 molecules. The peptide is then placed in the box of water, and the molecules that overlap with the peptide are removed. Counterions and any additional ions should be added at this time. They can be added by replacing water molecules. 3. For simulations in micelles, coordinates exist for two common types of micelles, DPC and SDS. DPC coordinates can be obtained from the web site of Professor Tuck Wong (http://www.chem.missouri.edu/wong/). SDS coordinates have been published by Alex MacKerell (36). The peptide is can be placed in the center of the micelle with the two centers of mass overlapping. This peptide–micelle complex is then solvated as described in Step 2. 4. A detailed method for building lipid bilayer simulations, with all necessary CHARMM scripts,


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is available on Benoit Roux’s web site (http://thallium. bsd.uchicago.edu/RouxLab/membrane.html). In this method, the bilayer is built around the peptides, with bad contacts between peptides and lipids or among lipid molecules reduced through a series of rotations and translations. Libraries of lipid conformations are available for a few common lipids, such as dipalmitoylphosphatidylcholine (DPPC). A brief summary of Roux’s method is outlined below: 4.1. Use sys1.inp to find the cross-sectional area of the peptide or oligomer. This information is necessary to determine the size of the lipid bilayer that will be needed. 4.2. Use sys2.inp to place dummy atoms into preliminary top and bottom leaflets. These atoms are replaced by the head group atoms of the lipids in subsequent steps. The height of the bilayer must be specified based on the length of lipids being used. 4.3. Sys3.inp minimizes the dummy atoms. 4.4. Sys4.inp requires the library of lipid conformers. In this step, each dummy atom is replaced with a lipid molecule. Each lipid is then systematically translated and rotated to remove bad contacts (such as overlapping atoms). 4.5. Use sys5.inp to minimize the system, which at this time is composed of peptide(s) and lipids. 4.6. Use sys6.inp and sys7.inp to make a sheet and then a box of water that is of the appropriate size for the system. Sys8.inp is then used to position the water box on each side of the bilayer. 4.7. Use sys9.inp to further minimize the system. 4.8. Additional minimization sys18.inp) can be used.

scripts

(sys10.inp

to

5. Create a.psf file for the fully constructed system. 3.2. Running a NAMD Simulation

1. Convert the prepared coordinate file to a NAMD.pdb file. This can be done using the program crd2pdb, which is available on the NAMD web site (http://www.ks.uiuc.edu/Research/namd/). 2. Convert the primary structure file (.psf) to a NAMD.psf file using charmm2namd, which is also available on the NAMD web site. 3. Create the simulation script. The following parameters need to be set (see Table 17.1): 3.1. Dimensions for the simulation box.

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Table 17.1 Description of each term to be specified in the NAMD script. Typical values for each term are given as well Term

Description

Typical value

Outputenergies

Number of time steps between energy outputs

1,000

xstFreq

Number of time steps between to the extended system coordinate file

1,000

dcdFreq

Number of time steps between writing to the trajectory file

1,000

wrapAll

Use periodic boundary conditions on all atoms

On

wrapNearest

Use nearest image to wrap the coordinates

On

rigidbonds

Fixes hydrogen bond lengths to the nominal value

All

timestep

Time step in femtoseconds

2

cutoff

Distance at which non-bonded and bonded interactions are cutoff

11

nonBondedFreq

Number of time steps between evaluation of the non-bonded interactions

1

fullElectFrequency

Number of time steps between evaluation of electrostatic interactions

1

pairlistdist

Distance between pairs for inclusion on the pairlist

14

stepsPerCycle

Number of time steps between atom reassignments

20

switching

Use switching for the non-bonded van der Waals interactions

On

switchDist

Distance at which the switching function should start to switch

8

exclude

Which pairs of bonded atoms to exclude

Scaled 1–4

1-4scaling

Constant factor to modify the electrostatic interactions for the pairs that are modified by exclude

1

langevin

Use Langevin dynamics

On

langevinDamping

Damping coefficient for Langevin dynamics

10

langevinTemp

Temperature for Langevin calculations

$temp

langevinHydrogen

Do not apply Langevin dynamics to hydrogens

No

langevinPiston

Use Langevin piston pressure control

On

langevinPistonTarget

Target pressure for Langevin piston pressure control

1.01325

langevinPistonPeriod

Barostat oscillation time in femtoseconds

200

langevinPistonDecay

Damping timescale in femtoseconds

10

langevinPistonTemp

Noise temperature

$temp

3.2. Pressure and temperature at which to run the simulation. 3.3. The number of time steps between each output (OutputEnergies, xstFreq, and dcdFreq). They


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need to be small enough to allow for capture of the details of interest in the simulation but large enough so that the trajectory file does not become too large for storage. 3.4. Specify cell basis vectors for periodic boundary conditions. For √ hexagonal cells, the vectors are [(a, 0, 0), (a/2, a 3/2, 0), (0, 0, h)] , where a is the width of the box (defined as the distance from the center of the simulation to the center of the adjacent image box) and h is the height. For rhombic dodecahedron cells, √ the vectors are [(a, 0, 0), (0, a, 0), (a/2, a/2, a 2/2)] , where a is the box length (defined as the distance from the center of the simulation to the center of the adjacent image box). 3.5. Turn on wrapAll and wrapNearest if using periodic boundary conditions. If wrapAll is specified, when a molecule leaves the simulation box, its coordinates are translated to the other side of the cell when they are output. If wrapNearest is specified, then the coordinates are wrapped to the nearest image to the origin, not the diagonal unit cell centered on the origin. 3.6. Turn on rigidbonds so that a 2 fs time step can be used. 3.7. Specify the cutoff distance. 3.8. Specify nonBondedFreq and fullElectFrequency (the number of steps between calculations of the non-bonded interactions). 3.9. Specify the distance for the pair list (pairlistdist). 3.10. Specify how often the pair list should be updated (Stepspercycle). 3.11. Turn on switching for the van der Waals interactions. 3.12. Specify the distance at which the switching function should be activated. 3.13. Specify which non-bonded interactions to exclude (typically exclude 1–2 and 1–3 bonded atoms from the non-bonded interactions). Also specify if the 1– 4 interactions should be scaled. 3.14. Set up the temperature and pressure controllers. Specify the Langevin damping coefficient, target pressure, piston oscillation period, and piston damping coefficient.

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3.15. Specify the particle mesh Ewald summation parameters. The function needs to be specified “on” and grid sizes must be provided. The grid should be chosen so that that there is approximately one point per Angstrom. 4. Minimize the system. The default minimization algorithm in NAMD combines conjugate gradient and line search methods. The amount of minimization necessary is dependent on the size of the system and how well the system was built. 5. Heat the system to the desired temperature. This should be done gradually. The Langevin piston is turned on and given a low temperature set point (usually less than 100 K). Langevin dynamics are run for a few thousand steps and then the temperature is gradually increased. Increasing by 30 K in each cycle to the final temperature set point should allow for the system to remain stable during the heating process. 6. Run the simulation. The simulation should be carried out until all properties of interest have stabilized.

4. Notes 1. There are a number of issues that can arise in the construction of the system. In particular, bad contacts can be built into the system in such a way that they cannot be overcome. In particular, one must be careful about the arrangement of lipid or detergent molecules near aromatic residues. The carbon chains can be placed so that they are inserted through the phenyl ring and will remain there for the duration of the simulation. Similar care must be taken for the position of the carbon chains near constrained loops, such as in ␤-hairpin peptides. 2. The initial configuration of the system is extremely important. There are still issues in the initialization of peptide– lipid systems because, in general, convergence of peptide– lipid systems is difficult to achieve due to the slow timescales on which the peptides are able to re-orient themselves when binding to the bilayer. Because of this, the proper orientation of the peptides at the start of the simulation is crucial. The need for prior knowledge of the binding conformation, and the restrictions on the accessible timescales, has hindered the predictive ability of lipid


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bilayer simulations. Specific information about the location of the peptide in a lipid bilayer is rarely available and so one has to assume a starting orientation and position for the peptide. This choice has a significant influence on the behavior of the peptide and on the conformation of the system at the end of the simulation. This problem can be overcome, in part, by using micelles. By starting with the peptide inside the micelle, the peptide “sees” the same surroundings regardless of the initial orientation (Fig. 17.3)

Fig. 17.3. Initialization issues. (a) For lipid bilayer simulations, the initial configuration has a strong bias on the final conformation observed. All three starting configurations should reach the same final conformation, the lower right, which is supported by experimental data. (b) For micelles, the final conformation can be reached with the peptide starting inside or outside the micelle, although again, it is unlikely to observe a peptide rotating while embedded into the micelle, so for simulations with the peptide starting outside of the micelle, the proper “face” must be positioned nearest the micelle surface. Using the conformation with the center of mass of the peptide overlapping the micelle center of mass reduces the bias.

3. Setup for systems can be done without using CHARMM. Scripts have been written for building systems using VMD (Visual Molecular Dynamics) and are available at the NAMD/VMD web site (http://www.ks.uiuc.edu/Research/vmd/). 4. The orientation of the simulation box vectors is different in CHARMM than in NAMD. For example, the hexagonal simulation box, recommended for lipid bilayer simulations, is rotated 15 degrees counterclockwise in CHARMM as compared to NAMD. Care must be taken in the start of the simulation of a system that has been built in CHARMM but is being run in NAMD. 5. The setup of the system should be checked visually at each step using VMD or Rasmol to ensure the proper orientation of molecules relative to each other.

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6. When constructing a lipid bilayer simulation for a pore, care must be taken in the initial stages to prevent the lipids from entering the interior of the pore. MMFP (miscellaneous mean field potential; see mmfp.doc in the CHARMM documentation) constraints are used in sys2.inp in the construction of any lipid bilayer to maintain the proper bilayer thickness. Cylindrical constraints can be used to prevent the lipids from entering the pore. 7. For simulations of peptides in water or interacting with micelles, the constant pressure–temperature ensemble is recommended. For lipid bilayer simulations, there is some discussion over the proper ensemble (46–48). Although the NPT (constant pressure–constant temperature) ensemble is used in most simulations, problems with the area per lipid can arise for lipid bilayer simulations. This is particularly true for simulations using CHARMM, for which NPz AT ensemble – where the area in the x–y plane is held constant but the z-dimension, normal to the bilayer, is allowed to fluctuate to retain constant pressure – or the NPγ T ensemble – where the surface tension is held constant – is recommended. In the simulations that have been presented in the literature, the simulation cell in NPT simulations using CHARMM or NAMD regularly shrinks, reducing the area per lipid. In 2004, Jensen and coworkers simulated a lipid bilayer containing 36 DPPC lipids per leaflet in the NPT ensemble and observed that the x–y dimensions of the cell decreased for the entire 15-ns simulation (49). Images of this system show an unrealistic expansion of the lipid in the z-direction, such that the two leaflets have separated. Feller and Pastor explained the unnatural behavior of lipid bilayers in simulations as being due to the small sizes of the bilayers that are studied (46). Long wavelength undulations of the bilayer are absent in small simulation cells, causing an increase in the surface tension above what would normally be expected from a macroscopic bilayer. The discussion on this topic is still open, but the options to run with constant area or a constant ratio of the x- and y-dimensions are available in NAMD. 8. For lipid bilayer simulations, the hydration of the lipids and the concentration of ions can have strong effects on the results. When experimental data are available, it should be matched as closely as possible. 9. Analysis can be done using CHARMM. A number of scripts for analysis of simulations are available in the script archive on the CHARMM Forum (www.charmm.org).


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Analysis will vary depending on the type of simulation carried out. 10. All simulations can provide information about the structure of the peptide. The secondary structure can be measured for each time point of the simulation by calculation of the dihedral angles. It is possible to compare the root mean square deviation of the peptide through the simulation to the initial structure or some other chosen structure. The dipole moment of the peptide is easily calculated, as well as the surface area. The area exposed to the solvent can also be easily determined. The shape of the peptide can be measured in terms of eccentricity or the maximum or average dimensions. The moment of inertia and radius of gyration are also easily calculated. The interaction energies between the residues within the peptide or the peptide and water can also be calculated and broken down further into the van der Waals interaction energy and the electrostatic interaction energy. Additionally, though hydrogen bonds are not explicitly modeled in CHARMM, the energy due to hydrogen bond interactions that have been defined by atom type, distance, and angle can be calculated. 11. Simulations in micelles allow for calculation of peptide properties as well as interaction energies (van der Waals and electrostatic) between peptide and self, peptide and micelle, or peptide and water. Hydrogen bond energy can also be calculated. Micelle shape can be analyzed over the course of the simulation, by monitoring the moments of inertia. 12. Radial distribution functions with micelle or bilayer core or head groups can provide information about the strength of interaction for each residue and the desired system component. 13. For bilayer simulations, properties such as thickness, tilt of lipids, order parameters, trans-gauche conformations, hydrogen bonding between head groups, and interactions with ions are often of importance. References 1. Allen, M. P. and Tildesley, D. J. (1987) Computer Simulations of Liquids. Oxford: Clarendon Press. 2. Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., III, DeBolt, S., Ferguson, D., Seibel, G., and Kollman, P. (1995) Amber, a computer program for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to elucidate the structures and

energies of molecules. Comp. Phys. Commun. 91, 1–41. 3. Jorgensen, W. L. and Tirado-Rives, J. (1988) The OPLS [optimized potentials for lipid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110, 1657–1666. 4. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and

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Langham and Kaznessis Karplus, M. (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics simulations. J. Comp. Chem. 4, 187–217. Berendsen, H. J. C., van der Spoel, D. L., and van Drunen, R. (1995) GROMACS: a message-passing parallel molecular dynamics implementation. Comp. Phys. Comm. 91, 43–56. Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kale, L., and Schulten, K. (2005) Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781–1802. Patra, M., Karttunen, M., Hyvönen, M. T., Falck, E., Lindqvist, P., and Vattulainen, I. (2003) Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions. Biophys J. 84, 3636–3645. Martyna, G. J., Tobias, D. J., and Klein, M. L. (1994) Constant pressure molecular dynamics algorithms. J. Chem. Phys. 101, 4177–4189. Feller, S. E., Zhang, Y., Pastor, R. W., and Brooks, B. R. (1995) Constant pressure molecular dynamics simulation: the Langevin piston method. J. Chem. Phys. 103, 4613–4621. Bhandarkar, M., Brunner, R., Chipot, C., Dalke, A., Dixit, S., Grayson, P., Gullingsrud, J., Gursoy, A., Hardy, D., Hénin, J., Humphrey, W., Hurwitz, D., Krawetz, N., Kumar, S., Nelson, M., Phillips, J., Shinozaki, A., Zheng, G., and Zhu, F. (2005) NAMD User’s Guide Version 2.6b1. Urbana: Theoretical Biophysics Group, University of Illinois and Beckman Institute. Leontiadou, H., Mark, A. E., and Marrink, S. J. (2006) Antimicrobial peptides in action. J. Am. Chem. Soc. 128, 12156–12161. Roux, B. and Simonson, T. (1999) Implicit solvent models. Biophys. Chem. 78, 1–20. Dominy, B. N. (1999) Parameterization and application of an implicit solvent model for macromolecules. Mol. Simulat. 24, 259–274. Brogden, K. A. (2005) Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria?. Nat. Rev. Microbiol. 3, 238–250. Kandasamy, S. K. and Larson, R. G. (2007) Binding modes of protegrin-1, a beta-strand antimicrobial peptide, in lipid bilayers. Mol. Simulat. 33, 799–807. Leontiadou, H., Mark, A. E., and Marrink, S. J. (2007) Ion transport across transmembrane pores. Biophys. J. 92, 4209–4215. Parvu, L. (2003) QSAR – a piece of drug design. J. Cell. Mol. Med. 7, 333–335.

18. Jenssen, H., Fjell, C. D., Cherkasov, A., and Hancock, R. E. (2008) QSAR modeling and computer-aided design of antimicrobial peptides. J. Pept. Sci. 14, 110–114. 19. Kaznessis, Y. N., Snow, M. E., and Blankley, C. J. (2001) Prediction of blood-brain partitioning using Monte Carlo simulations of molecules in water. J. Comput. Aid. Mol. Des. 15, 697–708. 20. Lejon, T., Stiberg, T., Strøm, M. B., and Svendsen, J. S. (2004) Prediction of antibiotic activity and synthesis of new pentadecapeptides based on lactoferricins. J. Pept. Sci. 10, 329–335. 21. Lejon, T., Strom, M. B., and Svendsen, J. S. (2001) Antibiotic activity of pentadecapeptides modelled from amino acid descriptors. J. Pept. Sci. 7, 74–81. 22. Lejon, T., Svendsen, J. S., and Haug, B. E. (2002) Simple parameterization of non-proteinogenic amino acids for QSAR of antibacterial peptides. J. Pept. Sci. 8, 302–306. 23. Marrero-Ponce, Y., Torrens, F., Alvarado, Y. J., and Rotondo, R. (2006) Bond-based global and local (bond, group and bondtype) quadratic indices and their applications to computer-aided molecular design. 1. QSPR studies of diverse sets of organic chemicals. J. Comput. Aid. Mol. Des. 20, 685–701. 24. Beswick, V., Guerois, R., CordierOchsenbein, F., Co¨ıc, Y. M., Tam, H. D., Tostain, J., Noël, J. P., Sanson, A., and Neumann, J. M. (1999) Dodecylphosphocholine micelles as a membrane-like environment: new results from NMR relaxation and paramagnetic relaxation enhancement analysis. Eur. Biophys. J. 28, 48–58. 25. Kallick, D. A., Tessmer, M. R., Watts, C. R., and Li, C. Y. (1995) The use of dodecylphosphocholine micelles in solution NMR. J. Magn. Reson. B 109, 60–65. 26. Kloosterman, D. A., Goodwin, J. T., Burton, P. S., Conradi, R. A., Stockman, B. J., Scahill, T. A., and Blinn, J. R. (2000) An NMR study of conformations of substituted dipeptides in dodecylphosphocholine micelles: implications for drug transport. Biopolymers 53, 396–410. 27. Lauterwein, J., Bösch, C., Brown, L. R., and Wüthrich, K. (1979) Physicochemical studies of the protein-lipid interactions in melittincontaining micelles. Biochim. Biophys. Acta 556, 244–264. 28. Fernandez, C. and Wuthrich, K. (2003) NMR solution structure determination of membrane proteins reconstituted in detergent micelles. FEBS Lett. 555, 144–150.

Antimicrobial Peptide Simulations 29. Rakitin, A. R. and Pack, G. R. (2004) Molecular dynamics simulations of ionic interactions with dodecyl sulfate micelles. J. Phys. Chem. B. 108, 2712–2716. 30. Wymore, T., Gao, X. F., and Wong, T. C. (1999) Molecular dynamics simulation of the structure and dynamics of a dodecylphosphocholine micelle in aqueous solution. J. Mol. Struct. 485, 195–210. 31. Wong, T. C. and Kamath, S. (2002) Molecular dynamics simulations of adrenocorticotropin (1–24) peptide in a solvated dodecylphosphocholine (DPC) micelle and in a dimyistoylphosphatidylcholine (DMPC) bilayer. J. Biomol. Struct. Dyn. 20, 39–57. 32. Tieleman, D. P., van der Spoel, D., and Berendsen, H. J. C. (2000) Molecular dynamics simulations of dodecylphosphocholine micelles at three different aggregate sizes: micellar structure and lipid chain relaxation. J. Phys. Chem. B 104, 6380–6388. 33. Shepherd, C. M., Schaus, K. A., Vogel, H. J., and Juffer, A. H. (2001) Molecular dynamics study of peptide-bilayer adsorption. Biophys. J. 80, 579–596. 34. Kandasamy, S. K. and Larson, R. G. (2004) Binding and insertion of alpha-helical antimicrobial peptides in POPC bilayers studied by molecular dynamics simulations. Chem. Phys. Lipids 132, 113–132. 35. Bruce, C. D., Berkowitz, M. L., Perera, L., and Forbes, M. D. E. (2002) Molecular dynamics simulation of sodium dodecyl sulfate micelle in water: micellar structural characteristics and counterion distribution. J. Phys. Chem. B. 106, 3788–3793. 36. MacKerell, A. D. (1995) Molecular dynamics simulation analysis of a sodium dodecyl sulfate micelle in aqueous solution: decreased fluidity of the micelle hydrocarbon interior. J. Phys. Chem. 99, 327–341. 37. Wymore, T. and Wong, T. C. (1999) Molecular dynamics study of substance P peptides partitioned in a sodium dodecylsulfate micelle. Biophys. J. 76, 1213–1227. 38. Yang, S. T., Yub Shin, S. Y., Kim, Y. C., Kim, Y., Hahm, K. S., and Kim, J. I. (2002) Conformation-dependent antibiotic activity of tritrpticin, a cathelicidin-derived antimi-

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Chapter 18 Computer-Based Analysis, Visualization, and Interpretation of Antimicrobial Peptide Activities Ralf Mikut Abstract This chapter describes a computer-based method for analyzing the quantitative structure–activity relationships (QSAR) of antimicrobial peptides. Quantitative or qualitative activity measurements and known peptide sequences are used as input for the analysis. The analysis steps consist of the preprocessing which specifically deals with dilution series from an assay with luminescent bacteria, transformation of quantitative activity values into activity classes, a feature extraction method using molecular descriptors for amino acids, feature selection methods, visualization strategies, the classifier model design for discrimination of active and inactive peptides, and the in silico design of promising new peptide candidates. Key words: Antimicrobial peptides, molecular descriptors, QSAR, data analysis.

1. Introduction The application of quantitative structure–activity relationship (QSAR) models (1) is a promising means of analyzing the relationship between a peptide sequence and its specific activities, such as antimicrobial action against single or groups of microbes, including Gram-positive or Gram-negative bacteria (2–4). For the data-based design of QSAR models, structural information about the peptide and its activity-related information are required. The structural information is mostly based on different kinds of features derived from atomic or molecular descriptors of the peptide sequence. Activity-related information can include the following:


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Mikut

1. A qualitative ranking based on a live/dead staining or zone of inhibition study that results in an “active–inactive” classification for each peptide. 2. A single quantitative measurement for each peptide, such as the minimal inhibitory concentration (MIC) of a substance, the half maximal inhibition (IC50) or an inhibition of 75% (IC75), and inhibitory concentrations relative to a control peptide (e.g., RelIC50, RelIC75). The peptide activity increases with lower values because the desired effect (e.g., a 75% inhibition of bacterial activity) occurs at a lower peptide concentration. 3. Separate activity measurements for different peptide concentrations in a dilution series. A typical example is luminescence measurements that indicate the remaining activity of luminescent bacteria exposed to different peptide concentrations, resulting from synthesis using SPOT technology (5). This assay is described in detail by Hilpert in this book (6). Especially in the case of dilution series, careful preprocessing and data validation are key to obtaining reliable results. A QSAR model can be optimized solely either for prediction power or for a compromise between prediction power and model simplicity. Both approaches require a large number of candidate features based on molecular descriptors. A compromise between prediction power and simplicity is based on drastic reduction of candidate features, using mathematical evaluation measures for feature selection (7). This chapter describes the complete analysis process, starting with preprocessing of the dilution series, followed by feature extraction using molecular descriptors, then feature selection, model design, and finishing with the in silico design of promising and novel peptide candidates. All steps can be computed using the Peptide Extension Package of the MATLAB Toolbox Gait-CAD (8) (see Section 3).

2. Materials In the design of a QSAR model for antimicrobial peptides, sequences of the investigated peptides (as one-letter code) and the activity-related information of each peptide are necessary. The latter information can be given in different forms (see Section 1) as follows: 1. A qualitative activity class as a text description (e.g., peptides are fully active, similar to positive control, worse than control, inactive) or by a numerical class code (e.g., “–1”

Computer-Based Analysis, Visualization, and Interpretation

289

for lower and “1” for higher activity relative to a positive control). Illustrative example: Sequence

Activity class

TQEHSNRWN

worse than control

KWRWRVKKR

fully active

2. A quantitative value characterizing activity in the form of a critical peptide concentration. Illustrative example: Sequence

IC75

TQEHSNRWN

0.4653

KWRWRVKKR

0.0491

3. A series of activity-related measurements, A(c), depending on the absolute or relative peptide concentration, c. These measurements should include a positive and negative control with known activity for each plate. A low A(c) value means a low bacterial activity and a high activity of the peptide. Illustrative example: Sequence

Plate

A(1)

A(0.5)

A(0.25)

A(0.125)

A(0.0625)

A(0)

TQEHSNRWN

1

10

2,000

10,000

9,850

10,000

9,900

KWRWRVKKR

1

25

46

63

142

1,696

10,000

Positive control

1

10

10

100

1,050

9,000

9,900

Negative control

1

8,000

8,500

8,800

9,500

9,800

10,000

3. Methods The following steps can be calculated using the Peptide Extension R Package of the MATLAB Toolbox Gait-CAD (8). MATLAB is a registered trademark of The MathWorks, Inc., Gait-CAD and the Peptide Extension Package are open source packages, licensed under the conditions of the GNU General Public License (GNU-GPL) of The Free Software Foundation. The download is available under http://sourceforge.net/projects/gaitcad. Both packages require MATLAB version 5.3 or later (see http://www.mathworks.com/). After starting MATLAB and Gait-CAD, a text file containing tabulator-separated values for peptide sequence and activityrelative information (see Section 2) can be imported by executing Peptides – Standard procedure (published in Humana Press Book) – Step 0 – Load data (see screenshot in Fig. 18.1). Sample files

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Fig. 18.1. Screenshot of the Peptide Extension Package from the MATLAB toolbox Gait-CAD.

for import are contained in the toolbox. After importing, Steps 1–15 can be performed by executing the related menu items. The results are shown as figures and protocol text files in the project directory. Parameters can be modified in the graphical user interface of the program: a reset to the proposed standard parameters is achieved by Peptides – Standard Procedure (published in Humana Press Book) – Restore standard parameters. The starting point for the following steps to applying a QSAR model depends on the type of activity information, as discussed in Section 2 (see Table 18.1). For example, the first three steps are only necessary if the activity is in the form of a dilution series. 1. It is assumed that bacterial activity is not positively correlated with peptide concentration. All data showing serious violations are handled as artifacts and are excluded from subsequent data analysis. We define a violation as a minimum increase of 30% of the activity value at lower concentrations and more than 1% of the maximal luminescence value in the study. Illustrative example: The maximal activity value recorded for a luminescent bacterium in a study is 10,000. For an activity value A(0.5) = 2,000 and concentration c = 0.5, a peptide is considered an artifact if the bacterial


291

Table 18.1 Necessary steps depending on different types of activity information Necessary steps in Section 3 1–3

4–5

6

Dilution series with control peptides

×

×

×

Dilution series without control peptides

×

7

× ×

×

RelIC75 activity values

× ×

×

Other activity values

8–15

× ×

Activity classes

activity at the next higher concentration (here: 1) is A(1) > 2,600 (30% increase, more than 0.01 × 10,000 = 100, see Fig. 18.2). For an activity value of A(0.5) = 100, concentration 0.5, the artifact limit is A(1) > 200 (more than 30% increase, more than 100). 2. In this next step, all smaller deviations from the assumptions of Step 1 are corrected. In order to avoid an increasing bacterial activity value with increasing peptide concentrations, each activity value is set to the maximum of all activity values for the same concentration, c, and of all activity values at higher concentrations.

4

Activity A

10

Peptide Positive control Negative control Artifact IC75 3

10 −2 10

−1

10 Concentration c

0

10

Fig. 18.2. Dilution series and associated bacterial activity with illustrative examples for one test peptide, one positive and one negative control, an artifact, and estimated IC75 values for the test peptide and the positive control.

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Illustrative example: A(0) = 9,900, A(0.0625) = 10,000, A(0.125) = 9,850, A(0.25) = 10,000, A(0.5) = 2,000, A(1) = 10 (see example in Fig. 18.2) is corrected to A(0) = 10,000, A(0.125) = 10,000. 3. The next aim is to calculate a single quantitative value that characterizes peptide activity from concentrationdependent bacterial activity values. For the computation of the IC75, we look for the two concentrations surrounding the IC75 (see Note 1) with values just below and above the 75% reduction. Between these two concentrations, the IC75 value is estimated using a logarithmic description of the activity values: I C75 = ((log10 (A(C1 )) − log10 (A I C75 )) ×c2 + (log10 (A I C75 ) − log10 (A(c2 )) ×c1 ))/(log10 (A(c1 )) − log10 (A(c2 ))) Illustrative example: The activity value AIC75 is calculated using 25% of the maximal concentration of the dilution series (here: A(0) = 10,000): AIC75 = 2,500. The value is located between c1 = 0.25 and c2 = 0.5. The result is IC75 = (log10 (10,000) – log10 (2,500)) × 0.5 + (log10 (2,500) – log10 (2,000)) × 0.25)/(log10 (10,000) – log10 (2,000)) = 0.4653 (see Fig. 18.2). 4. The IC75 value of each peptide is then compared with the IC75 of the positive control on the same plate (see Note 2). The relative value, RelIC75, is computed by dividing the IC75 of each peptide by the IC75 on the same plate: RelIC75 = IC75/IC75 (positive control). A peptide with RelIC75 = 1 has the same activity as the positive control; smaller values indicate a stronger activity. Illustrative example: On Plate 1, the IC75 value for the positive control is 0.1. The IC75 of a test peptide on the same plate is 0.4653. Consequently, the test peptide’s RelIC75 value is 4.653, which indicates lower activity than the positive control. 5. All plates must be handled as artifact and discarded from the analysis when they exhibit extreme deviations from the IC75 of the positive control or value A(1) of the negative control. An extreme IC75 deviation of a positive control is defined by less than 50% and more than 200% of the median value of all positive controls. An extreme deviation for A(1) of a negative control is defined by a value smaller than 25% of the median A(1) of all negative controls. The median value is the value separating the lower and higher half of a group of values.


293

Illustrative example: The median of all IC75 values is 0.08 for the positive control, and the median of the activity values for the negative control A(1) = 8,000. All plates with an IC75 value for the positive control larger than 0.16 and lower than 0.04 or an activity value for the negative control A(1) < 2,000 are labeled as artifact. 6. We recommend four different classes using the RelIC75 and the luminescence value A(1) of test peptides. These classes are “fully active” (RelIC75 ≤ 0.5), “similar to positive control” (0.5 < RelIC75 ≤ 2), “worse than control” (2 < RelIC75 ≤ 20), and “inactive” (RelIC75 > 20 or A(1) > 0.9 × A(1) of the negative control on the same plate). In the case of a dilution series, the additional condition A(1) of a peptide larger than 0.9 × A(1) of the negative control ensures that peptides without a relevant luminescence reduction are classified as inactive. This condition helps to handle plates with anomalous values, such as an unusually high IC75 value for the positive control. Illustrative example: A peptide with a RelIC75 value of 4.653 is classified as “worse than control”; if the negative control on a plate has an activity of A(1) = 8,000, all peptides with A(1) > 7,200 on the same plate are classified as inactive. 7. In the event that different forms of a quantitative value result from 2. In Sections 1 and 2, the class definition differs slightly. Here, a meaningful class definition must be established together with the design of each experiment. While class names can be the same, the values have to be defined relative to the corresponding values of a known positive control (similar to Step 6). Illustrative example: An alternative class definition uses MIC values instead of RelIC75 values. A known positive control has a MIC value of 0.4; in the experimental design, MIC values lower than 0.2 were defined as fully active; therefore, a peptide with a MIC value of 0.1 is assigned to the class “fully active.” 8. The following steps extract structural information from the peptide sequences. Besides the sequence itself, molecular descriptors can be used for assigning corresponding descriptor values to each amino acid. Typical molecular descriptors include the isoelectric point, the hydrophobicity following the Hopp–Woods scale or the Goldman– Engelmann–Steitz scale, molecular mass (all values according to (9)), or the Octanol-Interface scale (10) to describe the behavior by the peptide interaction with membranes (see Table 18.2 and Note 3). New peptide sequences are

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Table 18.2 Molecular descriptors for amino acids Isoelectric point

Hopp– woods

Goldman– Engelman– Molecular Steitz mass

OctanolInterface scale

Name

Symbol

Alanine

A

6.01

–0.50

–1.60

89.00

Arginine

R

10.76

3.00

12.30

174.00

1

Asparagine

N

5.41

0.20

4.80

132.00

2.41

Aspartic acid

D

2.77

3.00

9.20

133.00

0.43

Cysteine

C

5.07

–1.00

–2.00

121.00

0.22

0.33

Glutamic acid

E

3.22

3.00

8.20

147.00

1.61

Glutamine

Q

5.65

0.20

4.10

146.00

0.19

Glycine

G

5.97

0.00

–1.00

75.00

1.14

Histidine

H

7.59

–0.50

3.00

155.00

–0.06

Isoleucine

I

6.02

–1.80

–3.10

131.00

–0.81

Leucine

L

5.98

–1.80

–2.80

131.00

–0.69

Lysine

K

9.74

3.00

8.80

146.00

1.81

Methionine

M

5.74

–1.30

–3.40

149.00

–0.44

Phenylalanine

F

5.48

–2.50

–3.70

165.00

–0.58

Proline

P

6.48

0.00

0.20

115.00

–0.31

Serine

S

5.68

0.30

–0.60

105.00

0.33

Threonine

T

5.87

–0.40

–1.20

119.00

0.11

Tryptophan

W

5.00

–3.40

–1.90

204.00

–0.24

Tyrosine

Y

5.66

–2.30

0.70

181.00

0.23

Valine

V

5.97

–1.50

–2.60

117.00

–0.53

generated by replacing the amino acids in a sequence with their corresponding molecular descriptors. Illustrative example: For a sequence KWRWRVKKR, the sequence of isoelectric point is (9.74, 5.00, 10.76, 5.00, 10.76, 5.97, 9.74, 9.74, 10.76). 9. In order to apply data analysis tools, features must be extracted from the sequences of amino acids or molecular descriptors. For the amino acid sequence, relative frequencies of amino acid n-mers in a sequence are calculated: we use always n = 1 (frequency of amino acids) and n = 2 (frequency of amino acid pairs). Mean values, minimal and maximal values, and standard deviations are computed for molecular descriptors (see Note 4). Illustrative example: Using sequence KWRWRVKKR, the frequencies of amino acids are 3/9 for K and R, 2/9


295

for W, and 1/9 for V. The frequencies of 2-mers are 2/8 for WR and 1/8 for KW, RW, RV, VK, KK, and KR. For the sequence of isoelectric points (9.74, 5.00, 10.76, 5.00, 10.76, 5.97, 9.74, 9.74, 10.76), the mean value is 8.61, the standard deviation is 2.37, the minimal value is 5.00, and the maximal value is 10.76. 10. Feature evaluation and selection can be performed using any statistical measure to analyze relevant differences between the different activity classes. For a fast check, a univariate analysis of variance for each feature and a multivariate analysis of variance for two and three features simultaneously (ANOVA, respectively, MANOVA) are sufficient. These measures evaluate the mean values of selected features for all peptides belonging to the different classes, the covariance matrices of these classes, and the total variance of the complete data set (see Note 5). Features with large distances between the mean values of different classes and small covariances within the classes are preferred. These methods are described in statistical textbooks (for reference see (11)), and they are implemented in many statistical software packages. Illustrative example: In the study (12), using 1,609 peptides, the standard deviation of the Hopp–Woods descriptor (ANOVA value 0.23) is detected as the best single feature, while the standard deviation of the Hopp– Woods descriptor and mean value of the isoelectric point are one promising pair of features for multivariate analysis (MANOVA value 0.26). 11. The best features of Step 10 are not always characterized by statistically relevant differences between activity classes. The relevance of generated best features should be analyzed using a non-parametric Wilcoxon rank sum test for class pairs, especially using the feature distributions of fully active peptides against peptides of all other classes. This test estimates the probability (p value) that the population of fully active peptides has an identical distribution to the populations of the three other classes describing less active peptides. The test results are more confident compared to a t test because most features do not fulfill the assumption of a normal distribution. Illustrative example: Using data from study (7), the relevance of different features (e.g., standard deviation of Hopp–Woods descriptor) is shown with a p value of 20)

5 1

1.5

2

2.5

3

Standard deviation of Hopp−Woods in the sequence

Fig. 18.3. Scatterplot showing the best features standard deviation for the sequence of Hopp–Woods, mean value of the sequence of isoelectric point; position of the mean value and the covariance matrix of the class “fully active” for the Bayes classifier (bolded ellipsoid with bolded cross).


297

13. Based on the two or three selected features, a Bayes classifier is designed to discriminate the classes. This technique is used to estimate the probability that a certain class is associated with given feature values and vice versa. For our scenario, an estimation of normal distributions containing parameters for mean values and the covariance matrix for each class is sufficient if the class regions in the figure according to Step 12 are approximately compact and normally distributed. The design of Bayes classifiers is described in statistical textbooks, such as (11), and is implemented in many statistical software packages. The classifier predicts group membership for each peptide. Illustrative example: Using the study in (12), mean values and covariance matrices for all classes are shown as ellipsoids in Fig. 18.3. The ellipsoid for the class “fully active” is bolded. 14. The generation of promising new peptides is achieved in two separate steps (#14 and #15 following). First, the amino acid distribution of the best peptides (e.g., the class “fully active”) is calculated. The peptide frequencies are added up, resulting in regions between 0 and 1 for each amino acid. To compute a new peptide candidate, a vector of random, equally distributed numbers with values between 0 and 1 is generated. This vector is translated into corresponding amino acids using the cumulated frequencies. Here, a tenfold of the desired number of promising peptide candidates after the final step is generated, e.g., 1,000 for 100 after Step 15. Illustrative example: In a hypothetical study, the class “fully active” has amino acid frequencies of 0.4 for R and W, 0.2 for K, and 0 for all other amino acids. The cumulated frequencies are 0.4 for R, 0.8 for W, 1 for K. To translate the random sequence, all values below 0.4 are set to R, all values between 0.4 and 0.8 to W and the rest to K. For a sequence of random numbers (0.95, 0.23, 0.61, 0.49, 0.89, 0.76, 0.45, 0.02, 0.82), the generated amino acid sequence is KRWWKWWRK. 15. In the last step of model peptide generation, using the sequences of the newly generated peptides from Step 14, the selected features according to Steps 8–11 are computed. Now, the Bayes classifier model from Step 13 can be applied to all generated peptides. With this model, the probability that a newly generated peptide belongs to the class of fully active peptides can be computed. The most promising peptides are the peptides with the highest probabilities for the class “fully active.” Finally, these peptides (e.g., the best 100/1,000 generated peptides in Step

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Mikut

14) are synthesized and their activity values are measured. These measurements are now used as input for Step 1, to begin a new iteration of peptide design.

4. Notes 1. Different alternatives for the chosen activity indicator or the methods for the computation are possible here; however, the more commonly used IC50 value is more sensitive against disturbances and oscillations of the luminescence values. The same problem occurs in model estimation of the four parameter model of Hill (13). 2. All luminescence experiments are very sensitive to differences in bacteria, peptide concentration, and purity, as well as the living conditions of the bacteria during the experiment (e.g., temperature, humidity). The proposed normalization strategy assumes similar bacteria concentrations and living conditions during one experiment for one plate. Consequently, all activity measures are based on relative measures according to the positive control. One drawback of this normalization method is a high sensitivity of RelIC75 to concentration differences in the positive control on different plates. 3. The molecular descriptors shown in Table 18.2 are only a small subset of possible scales. As examples, other hydrophobicity scales (see values from (9)), membrane-oriented scales (10), or scales based on a principal component analysis of other molecular descriptors (2, 15) can be used. In addition, atomic descriptors (3) or features to describe threedimensional characteristics (16) can be included. 4. Mean, minimum, maximum, and standard deviation values for the whole sequence are only the simplest features used to extract sequence information. One further option is frequencies of fuzzy terms (7). In addition, the descriptors can be analyzed for each position in a sequence or as segments, such as the first or last two amino acids (12). 5. These evaluation measures are only reliable if all classes are covered by a sufficient number of peptides. Under normal conditions, each class should include more than 50 peptides. A formal statistical evaluation of the results is difficult due to the large candidate feature set after feature extraction, resulting from Step 8. A strong evaluation would require the use of Bonferroni-like corrections for multiple tests. Since the features used in the model are strongly correlated, this leads


299

to extremely conservative results due to an overestimation of the degrees of freedom. The best way to compensate for this is the extraction of candidate features, the model-based design of promising peptides, and its verification by a newly synthesized library. The evaluation of features using univariate or multivariate analysis of variance is only one possible option. Another alternative is a regression model, which regresses activity with the candidate features. References 1. Perkins, R., Fang, H., Tong, W., and Welsh, W. (2003) Quantitative structure-activity relationship methods: perspectives on drug discovery and toxicology. Environ. Toxicol. Chem. 22, 1666–1679. 2. Hellberg, S., Sjostrom, M., Skagerberg, B., and Wold, S. (1987) Peptide quantitative structure-activity relationships, a multivariate approach. J. Med. Chem. 30, 1126–1235. 3. Cherkasov, A., Hilpert, K., Jenssen, H., Fjell, C. D., Waldbrook, M., Mullaly, S. C., Volkmer, R., and Hancock, R. E. (2008) Use of artificial intelligence in the design of small peptide antibiotics effective against a broad spectrum of highly antibiotic-resistant superbugs. ACS Chem. Biol., 4, 65–74. 4. Frecer, V. (2006) QSAR analysis of antimicrobial and haemolytic effects of cyclic cationic antimicrobial peptides derived from protegrin-1. Bioorgan. Med. Chem. 14, 6065–6674. 5. Hilpert, K., Winkler, D. F. H., and Hancock, R. E. W. (2007) Peptide arrays on cellulose support: SPOT synthesis – a time and cost efficient method for synthesis of large numbers of peptides in a parallel and addressable fashion. Nat. Protoc. 2, 1333–1349. 6. Hilpert, K. (2009) High-throughput screening for antimicrobial peptides using the SPOT Technique. In Part II: Analysis, Properties, and Mechanisms of Antimicrobial Peptides (from this book). 7. Mikut, R. and Hilpert, K. (2009) Interpretable features for the activity prediction of short antimicrobial peptides using fuzzy logic. Int. J. Pept. Res. Ther. 15 (2), 129–137.

8. Mikut, R., Burmeister, O., Braun, S., and Reischl, M. (2008a). The open source MATLAB toolbox Gait-CAD and its application to bioelectric signal processing. In Proceedings of DGBMT-Workshop Biosignal Analysis, Potsdam, 109–111. 9. Hildebrand, P. (2006). Zur Strukturvorhersage der Membranproteine. PhD thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät. 10. White, S. and Wimley, W. (1999) Membrane protein folding and stability: physical principles. Annu. Rev. Biophys. Biomol. Struct. 28, 319–365. 11. Tatsuoka, M. M. (1988) Multivariate Analysis. New York: Mac Millan. 12. Mikut, R., Reischl, M., Ulrich, A., and Hilpert, K. (2008b). Data-based activity analysis and interpretation of small antibacterial peptides. In Proceedings of the 18th Workshop Computational Intelligence, Universitätsverlag Karlsruhe, 189–203. 13. DeLean, A. (1978) Simultaneous analysis of families of sigmoidal curves: application to bioassay, radioligand assay, and physiological dose-response curves. Am. J. Physiol. Gastr. L. Physiol. 235, 97–102. 14. Sandberg, M., Eriksson, L., Jonsson, J., Sjostrom, M., and Wold, S. (1998) New chemical descriptors relevant for the design of biologically active peptides: a multivariate characterization of 87 amino acids. J. Med. Chem. 41, 2481–2491. 15. Mekenyan, O., Nikolova, N., and Schmieder, P. (2003) Dynamic 3D QSAR techniques: applications in toxicology. J. Mol. Struct. THEOCHEM 622, 147–165.

Section III Antimicrobial Peptides as Therapeutic Agents

Chapter 19 Potential Therapeutic Application of Host Defense Peptides Lijuan Zhang and Timothy J. Falla Abstract Host defense peptides (HDPs) are relatively small, mostly cationic, amphipathic, and of variable length, sequence, and structure. The majority of these peptides exhibit broad-spectrum antimicrobial activity and often activity against viruses and some cancer cell lines. In addition, HDPs also provide a range of immunomodulatory activities related to innate immunity defense, inflammation, and wound healing. The development of these multi-faceted molecules and their bioactivities into clinically important therapeutics is being pursued using a number of different approaches. Here we review the role of HDPs in nature and application of this role to the development of novel therapeutics. Key words: Host defense peptides, HDPs, antimicrobial peptides, anti-infectives, antifungals, anti-sepsis, topical therapeutics, immunomodulators.

1. Introduction Host defense peptides (HDPs), traditionally referred to as antimicrobial peptides, are ribosomally synthesized, relatively small (10-fold) during a 6-h study period. Treatment with NZ2114 caused a significantly higher reduction in CSF bacterial concentrations as compared to therapy with ceftriaxone (107). Also, significantly more rabbits had sterile CSF at 5 and 10 h when treated with NZ2114 as compared to therapy with ceftriaxone (107). Novozymes entered in December 2008 a global licensing and collaboration agreement with Sanofi-Aventis for the development and marketing of NZ2114 for the treatment of severe infections such as pneumonia, septicemia, and complicated skin and soft tissue infections.

3.14. Pacgen Biopharmaceuticals

Pacgen Biopharmaceuticals Corporation (www.pacgenbiopharm. com) focuses on the development of peptide/protein-based therapeutics for the treatment of infectious and inflammatory diseases. The company’s lead compound, PAC-113, is an antifungal peptide in Phase II clinical trials for the treatment of oral candidiasis. The peptide is based on histatin technology initially developed by Demgen Pharmaceuticals (Pittsburgh, PA). Pacgen recently reported positive results from its Phase IIb dose-ranging clinical trial of PAC-113.

3.15. PolyMedix

PolyMedix (www.polymedix.com) is currently advancing a de novo drug design approach to design small molecule compounds that mimic or regulate the activity of protein targets. PMX-30063

322

Zhang and Falla

was designed to mimic the amphiphilic structure of defensin, but in the form of a synthetic, non-peptide, small molecule structure. It is bactericidal and kills microbes by direct biophysical disruption of the bacterial cell membrane. It is active against both Gram-positive and Gram-negative bacteria, in particular against 146 different strains of Staphylococcus including clinical isolates of multiple vancomycin and methicillin-resistant strains. An efficacious systemic dose of 2 mg/kg BID in the mouse S. aureus thigh model PMX-30063 has received approval in 2008 from Health Canada for a Phase I clinical trial to assess safety for treatment of systemic infections. In preclinical toxicology testing the NOAEL (no observable adverse effect level) was found to be 24 mg/kg/day for PMX-30063 which provides potential for a meaningful therapeutic index in the clinic. 3.16. Polyphor Ltd

Polyphor Ltd (www.polyphor.com) developed peptide mimetics of ␤-sheet HDPs, such as protegrin-1, creating, for example, POL-7080, which has selective activity toward Gram-negative bacteria and, in particular, Pseudomonas spp. (108). The compound is currently in preclinical development for the treatment of Pseudomonas infections.

References 1. Reddy, K. V., Yedery, R. D., and Aranha, C. (2004) Antimicrobial peptides: premises and promises. Int. J. Antimicrob. Agents 24, 536–547. 2. Hancock, R. E. (1997) Peptide antibiotics. Lancet 349, 418–422. 3. Toke, O. (2005) Antimicrobial peptides: new candidates in the fight against bacterial infections. Biopolymers 80, 717–735. 4. Toke, O., Cegelski, L., and Schaefer, J. (2006) Peptide antibiotics in action: investigation of polypeptide chains in insoluble environments by rotational-echo double resonance. Biochim. Biophys. Acta 1758, 1314–1329. 5. Selsted, M. E., Novotny, M. J., Morris, W. L., Tang, Y. Q., Smith, W., and Cullor, J. S. (1992) Indolicidin, a novel bactericidal tridecapeptide amide from neutrophils. J. Biol. Chem. 267, 4292–4295. 6. Rozek, A., Friedrich, C. L., and Hancock, R. E. (2000) Structure of the bovine antimicrobial peptide indolicidin bound to dodecylphosphocholine and sodium dodecyl sulfate micelles. Biochemistry 39, 15765–15774. 7. Askou, H. J., Jakobsen, R. N., and Fojan, P. (2008) An atomic force microscopy study of the interactions between indolicidin and sup-

8.

9.

10. 11.

12.

13.

ported planar bilayers. J. Nanosci. Nanotechnol. 8, 4360–4369. Shaw, J. E., Alattia, J. R., Verity, J. E., Prive, G. G., and Yip, C. M. (2006) Mechanisms of antimicrobial peptide action: studies of indolicidin assembly at model membrane interfaces by in situ atomic force microscopy. J. Struct. Biol. 154, 42–58. Shaw, J. E., Epand, R. F., Hsu, J. C., Mo, G. C., Epand, R. M., and Yip, C. M. (2008) Cationic peptide-induced remodelling of model membranes: direct visualization by in situ atomic force microscopy. J. Struct. Biol. 162, 121–138. Otvos, L., Jr. (2005) Antibacterial peptides and proteins with multiple cellular targets. J. Pept. Sci. 11, 697–706. Selsted, M. E. and Ouellette, A. J. (2005) Mammalian defensins in the antimicrobial immune response. Nat. Immunol. 6, 551–557. Radhakrishnan, Y., Hamil, K. G., Yenugu, S., Young, S. L., French, F. S., and Hall, S. H. (2005) Identification, characterization, and evolution of a primate beta-defensin gene cluster. Genes Immun. 6, 203–210. Zanetti, M., Gennaro, R., and Romeo, D. (1995) Cathelicidins: a novel protein family with a common proregion and a variable

Potential Therapeutic Application of Host Defense Peptides

14.

15.

16.

17.

18.

19.

20.

21.

22.

23.

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Chapter 20 Therapeutic Potential of HDPs as Immunomodulatory Agents ˚ Havard Jenssen and Robert E.W. Hancock Abstract One of the most significant advances in medical history is the discovery and development of antibiotics, which in the middle of last century was flourishing and appeared to be the ultimate solution to the treatment of life-threatening human bacterial diseases. However, lately there has been a huge decline in the rate of discovery of new antimicrobial intervention strategies in parallel with an increasing incidence of multidrug-resistant pathogens; if these circumstances do not change we will continue to approach the end of the antibiotic era. Facing this dark future, scientists are considering new strategies for intervention tailored around the appropriate (selective) stimulation of the host’s immune system, and particularly rapid acting innate immunity, as an alternative to direct targeting of microbial pathogens. One recent player in such an immunomodulatory strategy is the naturally occurring host defence peptides (HDP) and their synthetic innate defence regulator (IDR) analogues. In this chapter, we will discuss the potential therapeutic use of HDPs and IDRs as immunomodulatory agents. Key words: Cationic host defence peptides, anti-infective therapy, antimicrobial peptides, innate defence regulators, immune stimulation, immunomodulator, anti-inflammatory.

1. Introduction The initiation of the therapeutic use of penicillin during the Second World War followed by the discovery and development of other antibiotics targeting bacterial, and later also viral and fungal pathogens, has undoubtedly had a tremendous impact on human life. However, recently there has been a tremendous decline in the discovery and development of new drugs, e.g. only three new chemical classes of antibacterials have entered the market in the past 40 years (i.e., lipopeptides, oxazolidinones and streptogramins, all targeting A. Giuliani, A.C. Rinaldi (eds.), Antimicrobial Peptides, Methods in Molecular Biology 618, DOI 10.1007/978-1-60761-594-1 20, © Springer Science+Business Media, LLC 2010

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Gram-positive infections), while the frequency of isolation of drug-resistant pathogens is rapidly increasing. Globally it is estimated that infectious diseases still account for one-third of all human deaths, and big players like respiratory infections, HIV, malaria, and tuberculosis are all found among the top eight killers (www.who.int/whosis/whostat/2008/en/index.html). A novel strategy for the development of new interventions is to target the host’s own immediate defence system, innate immunity. However, the development of drugs targeting the innate immune system has experienced some difficulties, and sceptics have argued against the potential of this strategy, largely due to the potential downside offered by inflammation (especially if too vigorous or too prolonged) and the complexity and consequent lack of mechanistic biological understanding of this defence machinery. Despite this there are several exciting potential targets for development of new anti-infectives and a number of targets are currently being targeted by different strategies, e.g. antibodies, biologicals including proteins and peptides, and small-molecule agonists and antagonists; the success of these ventures has been reviewed elsewhere (1–6). Another promising drug class is socalled host defence peptides (HDPs; also termed cationic antimicrobial peptides – AMPs when they have direct antimicrobial activity) and synthetic derivative thereof. The therapeutic use and potential of these HDPs as potential anti-infective immunemodulators are discussed in detail in this chapter.

2. Targeting the Host Innate Immune System

To prevent and cure infections by targeting the innate immune system is an innovative but ambitious idea. This intrinsically complex and conserved signalling system has developed throughout evolution to respond and defeat all types of infections. It is highly effective, given our constant exposure to pathogens but relatively infrequent symptomatic infections; at the same time it is delicately tuned such that it seldom results in prolonged inflammation. The strategy of designing anti-infectives for selective modulation of the innate immune defence system has been made possible by the discovery of specific pathogen recognition receptors, such as Toll-like receptors, and intracellular sensors of microbial components such as the Nod-like receptors and retinoic-acid inducible gene I-like receptors (7). Exposure to pathogenic signalling molecules results in a rapid response that normally returns to homeostasis within hours to days; if unsuccessful in clearing the infection a smooth transition to adaptive (acquired immunity) occurs. However, under some circumstances this control

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of inflammation can break down and/or uncontrolled so-called chronic inflammation can ensue; if the inflammatory response is too vigorous or maintained for a prolonged period of time it may lead to pathological consequences and many human disease syndromes demonstrate the symptoms of uncontrolled inflammation including excessive bleeding and chronic pain. Hence the optimal anti-infective therapy based on innate immunity should employ tailored immunomodulators that offer the potential to tip the balance back in favour of the host, by either (selectively) boosting or inhibiting selected elements of the immune response at the same time as exploiting and enhancing the efficiency of the powerful and multifaceted effector mechanisms that have evolved specifically for the purpose of pathogen clearance. It is also important to remember that there are many aspects of the pathogen-sensing, response and control mechanisms that we do not understand, giving hope that in the future even more novel targets for anti-infective therapies will be revealed to assist us in facing the increasing drug resistance challenge. New knowledge and sophisticated technological advances will help accelerate the development of novel anti-infective immunomodulators, e.g. systems biology approaches, genomic libraries for siRNA gene silencing, the high-throughput development of gene knockout mice, studies of single-nucleotide polymorphisms associated with disease and the profiling of transcriptional, micro-RNA and protein interaction networks will all promote new insights into innate immune response mechanisms (8, 9). In this regard, a recently launched powerful tool is the publicly-available bioinformatics resource, Innate DB (www.innatedb.com) (10) and IIDB (http://db.systemsbiology.net/IIDB) (11), which are innate immunity-specific databases that include data analysis resources to facilitate the functional analysis of innate immunity responses, as well as the IIPGA program (www.innateimmunity.net), which is a collaborative effort to analyse polymorphisms in human innate immunity genes.

3. Host Defence Peptides The constant battle between the host and the pathogens through evolution has resulted in a finely tuned defence system involving innate (germ line encoded) and adaptive (antigen specific due to gene rearrangements and acquired due to pathogenic challenge) immunity. Host defence peptides have been demonstrated to play a pivotal role in the orchestration of innate immune and inflammatory responses of mammals, amphibians, and insects (12–14). Recently, increasing evidence is supporting the

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involvement of these antimicrobial peptides in bridging these two immune defence strategies. Being key players in the fundamental interplay between host and microbe makes these HDPs/AMPs signature molecules of host defence exhibiting substantial diversity even within a single host and occurring in moderate to high concentrations. Virtually all species of life produce them, with more than 1,000 natural occurring peptides having been described to date, and the majority of these are described in databases for eukaryotic host defence peptides: e.g. the site at the University of Trieste (http://www.bbcm.units.it/∼tossi/pag1.htm) and the AMPer site (http://www.cnbi2.com/cgi-bin/amp.pl) (15). These peptides generally fall into four major structural categories based on their amphiphilic conformations that often occur only after membrane interaction; namely ␤-structures with two to four ␤-strands and amphipathic ␣-helices, and less commonly loop and extended structures (Fig. 20.1). These peptides are typically short (12–50 amino acids), carrying a net positively charged (+ 2 to 9) due to excess basic arginine and/or lysine residues, and contain up to 50% hydrophobic amino acids (permitting membrane interaction and enabling membrane damage and/or cell penetration). Although their potency varies substantially, depending in part on antagonism by physiological concentrations of mono- and divalent cations and polyanions they often have broad spectra of activity that can encompass antibacterial, antifungal, antiviral and anti-parasitic activities (16). Equally important is

Fig. 20.1. Structural classes of antimicrobial peptides. (A) Mixed structure of human ␤-defensin-2 (HBD-2) (PDB code 1FQQ) (82), (B) looped thanatin (PDB code 8TFV) (83), (C) ␣-helical human cathelicidin LL-37 (PDB code 2k6o) (84), (D) extended indolicidin (PDB code 1G89) (85). The figures have been prepared with use of the graphic program MolMol 2 K.1 (86).


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their ability to recruit and activate or modulate effectors of the innate immune system (14, 17).

4. Host Defence Peptides Mode of Action

Initially cationic peptides were investigated due to their direct antimicrobial activity. Though the peptides usually demonstrate lower potency than conventional antibiotics, one strength lies in their ability to kill multidrug-resistant bacteria. They are able to act extremely rapidly and can engage and inhibit multiple bacterial targets (18). Initially the peptides were believed to act only by perforating bacterial membranes through, e.g. “aggregate” (19), “toroidal pore” (20–23), “barrel-stave” (24) or “carpet” mechanistic models (25). Later studies also demonstrated the ability of many peptides to translocate across the cytoplasmic membrane of bacteria (26) targeting DNA/RNA synthesis (27–30), protein synthesis (28, 29, 31, 32), enzymatic activities (33, 34) and cell wall regeneration (35) among others. In addition to this direct antimicrobial activity, there is strong evidence that a broad range of cationic peptides can stimulate the host immune system as a mode of promoting pathogen clearance, thus giving rise to the new term host defence peptides (HDPs) (Fig. 20.2). The terms AMPs and HDPs are to some extent interchangeable, though the term HDPs is used here for natural peptides with known immunomodulatory properties, while AMPs are known for their direct antimicrobial effects; however, a single peptide may have both features. For example, human peptides are likely directly antimicrobial when found in high concentrations (e.g. in neutrophil granules or in the crypts of the intestine) and exhibit prominent immunomodulatory properties when found at lower concentrations, e.g. after release and dissemination from these sites, e.g. at mucosal surfaces. There are several examples indicating that HDPs are key players in innate immunity. For example, inflammatory bowel disease, also known as Crohn’s disease, is generally characterized by chronic inflammation of the intestine, commonly in the distal ileum and/or colon (36). Recent studies have demonstrated that patients suffering from Crohn’s disease have a deficiency in the epithelial cell secretion of ␤-defensins (i.e. human ␤-defensins 2 and 3) (37, 38) as well as expression of human cathelicidin LL-37 (39). This results in an imbalance between luminal bacteria and the HDP concentrations, allowing intestinal bacteria from the microbial flora to trigger inflammation with associated adherence and invasion into the mucosa (40). HDP expression in the skin is also known to protect against invasive bacterial infections. Transgenic mice

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Fig. 20.2. Immunomodulatory properties of host defense peptides. The figure illustrates possible targets at the systemic level (left) and in a single cell (right). Several HDPs’, e.g. LL-37, CRAMP, Indolicidin and SMAP-29 can alter toll like receptor-induced responses, e.g. suppress the expression of pro-inflammatory molecules (e.g. tumor necrosis factor ␣) and inhibit apoptosis of neutrophils (A & B) (47, 51, 87–91). Dendritic cell differentiation may be targeted (C) (92) as well as several steps in the maturation and differentiation of monocytes to macrophages (D & E). LL-37 activates macrophages (F), leading to release of effector molecules, primarily chemokines. These chemokines, as well as HDP’s alone (e.g. CRAMP, HNP-1, HNP-2, LL-37), promotes chemotaxis and migration of leukocytes to the afflicted area (G) (93–97). LL-37 promotes the expression of co-stimulatory molecules on dendritic cell and promotes expression of Th 1 cytokine interleukin-12 (H). Several immune cells are know to be targeted by HDPs. Cell signalling may be affected at several levels in the signalling cascade (I) (73, 98), interfering with gene transcription (J), altering the cellular levels of different effector molecules and cellular degranulation (K) (47, 88, 89, 92, 99–103). The figure is reprinted and modified from Hamill et al., 2008 (1) with permission from authors and Current Opinion in Biotechnology, Copyright © 2008, Elsevier.

mutated in the gene for the mouse peptide CRAMP, a homolog of human LL-37 (41, 42), have been observed to develop significantly more severe skin infections than control mice, though the isolated leukocytes from these CRAMP-deficient mice were functionally competent and similar to wild-type leukocytes (43). Similarly, patients suffering from morbus Kostmann disease and associated severe gum inflammation have an associated deficiency in neutrophil levels of LL-37, as well as reduced concentrations of ␣-defensins (i.e. human neutrophil peptides-1, -2 and -3) (44). Similarly the ability of peptides to mediate the attraction of various immune cell types (either directly as chemokines or indirectly by stimulating epithelial and monocytic cells to secrete conventional chemokines) to demonstrate anti-inflammatory/antiendotoxic activity, stimulate blood vessel growth (angiogenesis),


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promote wound healing, and promote and polarize adaptive immune responses have all been demonstrated in mouse models and human or mouse tissue or cell systems (43, 45–52). Indeed it can be argued that the systemic effects found with any cationic peptide may be primarily due to the often-undescribed immunomodulatory properties of the peptide, given that the direct antimicrobial activity of peptides, but usually not their immunomodulatory activities, is strongly antagonized by physiological salt concentrations, i.e. 100 mM monovalent- and 2 mM divalent cations (as well as polyanions like glycosaminoglycans such as heparin) (46). In our view the systemic action of peptides that are deliberately added for therapeutic purposes may involve either direct (i.e. antibiotic) or indirect (i.e. immunomodulatory) antimicrobial activity. For example, the most clinically advanced peptide developed by Migenix, primarily as an antimicrobial, has recently been demonstrated to have activity in phase III clinical trails in preventing catheter-associated tunnel infections, as well as activity against the inflammatory disease Rosacea, for which there is no microbial association (Table 20.1).

5. Commercial Production of Host Defence Peptides

The clinical use of HDPs has been limited by issues like cost of goods. Several commercial participants have tried to circumvent this issue by moving from traditional solid-phase synthesis to solution-phase methods, and further to a hybrid methodology, e.g. a convergent strategy of synthesizing peptides, i.e., selecting peptide segments and assembling them together typically using a solution phase methodology. The best example of this is Roche (http://www.roche.com/index.htm) and Trimeris’ (http://www.trimeris.com) joint success in large-scale production of the HIV fusion inhibitor, enfuvirtide (Fuzeon, T-20), by solid- and solution phase hybrid synthesis (53, 54). Enfuvirtide is a 36-amino-acid peptide that binds to a region of the HIV envelope glycoprotein gp41, thus blocking viral entry into CD4+ T cells. The drug is licensed for use in patients in whom other HIV medications are losing effectiveness, in part due to the limited annual production capacity (3.7 metric tons in 2005 providing treatment for ∼47,000 patients). Aside from traditional peptide synthesis, other biotechnological approaches may be used for commercial production of HDPs, e.g. recombinant systems built on bacterial-, fungalor mammalian-expression platforms. Novozymes (Bagsvœrd, Denmark, http://www.novozymes.com/en) have demonstrated great success using a fungal-based system to recombinantly

R Omiganan / CP-226/ MBI-226/ CLS001

ILRWPWWPWRRK-CONH2

Phase III : Analogue of bovine AMP (indolicidin). Omiganan has been demonstrated in Phase II trials to have anti-inflammatory properties vs. Rosacea and acne Phase IIIb: Direct antibacterial properties for prevention of catheter related infections.

Phase IIa: A 9-mer peptide derived from a human HDP (bactericidal/permeability-increasing protein). Developed as a topical gel for treatment of common skin disease, impetigo, with demonstrated potent antibacterial activity against several difficult-to-control bacterial strains including methicillin-resistant Staphylococcus aureus Note: The XOMA 629 development program was recently suspended (Press release 10 November 2008)

KLFR-(D-naph-A)-QAK-(Dnaph-A)

XOMA 629/XMP.629

PAC-113

GFGC1 NGPWDEDDMQC2 HNHC3 Preclinical: A variant of plectasin which has KSIKGYKGGYC1 AKGGFVC2 KC3 Ydemonstrated potent Gram-positive effect in COOH (Plectasin) systemic pneumococcal and streptococcal infections AKRHHGYKRKFH-CONH2 Phase IIb : A 12-mer segment present in histatin 3 and 5, which reduces oral candidiasis (0.15% mouth rinse formulation)

Plectasin NZ2114

Description/status/results

Sequence

Drug

Table 20.1 Immunomodulatory and antimicrobial peptides in clinical trials or developmental stages

Migenix/Cutanea (Vancouver, BC, Canada), www.migenix.com, www.cutanealife.com (105)

XOMA (Berkeley, CA, USA), www.xoma.com (104)

Pacgen (Vancouver, BC, Canada), www.pacgenbiopharm.com

Novozymes AS/Sanofi-Aventis (Bagsvœrd, Denmark), www.novozymes.com

Company & reference

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Phase IIb: A synthetic 8-mer peptide derived from ␣-melanocyte-stimulating hormone. Inhibits vulvovaginal candidiasis, commonly known as vaginal yeast infection

(Ac-CKPV-CONH2 )2

SIQDLNVSMKLFRKQAKWKIIV KLNDGRELSLD-COOH

KLFKRHLKWKII-CONH2

CZEN-002

PTX002

PTX005/SC4

PepTx (St. Paul, MN, USA), www.peptx.com (106, 107)

Zengen/Zensano (Woodland Hills, CA, USA), www.biospace.com

AM-Pharma (Bunnvik, The Netherlands), www.ampharma.com

Inimex (Burnaby, BC, Canada), www.inimexpharma.com

Note: Amino-acid sequences are given in one-letter code. Cysteines forming disulfide bonds are numbered with subscripts to indicate their pairings. N- and C-terminal modifications are indicated before the hyphen in the front or after the hyphen at the end of the sequence.

Discovery phase: 33-mer peptide with two distinct ␤-sheet folds and a 12-mer peptide derivative thereof. Has demonstrated broad-spectrum antimicrobial and antiendotoxin neutralizing activity in both in vitro and in vivo experiments

Phase IIa: N-terminal fragment of human HDP (lactoferrin) has indicated immunomodulatory activity. Trials address allogeneic bone marrow stem cell transplantation–associated infections and other drug resistant hospital acquired infections

GRRRRSVQWCA-COOH

hLF1-11

Preclinical: 5-mer peptide modelled on IDR-1. IDR-1 was demonstrated to work through selective stimulation of innate immunity, up-regulating protective immunity while suppressing pro-inflammatory cytokine production in response to bacterial TLR agonists

KSRIVPAIPVSLL-CONH2 (IDR-1)

IMX942

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produce plectasin in large scale with therapeutic purity under good manufacturing practice (GMP) conditions (55). Plectasin is a fungal defensin-like 40-amino-acid peptide, with broadspectrum antibacterial activity (56) and no affect on cell viability or interleukin-8 production (57). A derivative of plectasin (Plectasin NZ2114) is currently in preclinical development as a very potent direct Gram-positive antimicrobial in a collaboration between Novozymes and Sanofi-Aventis (Bridgewater, NJ, USA) (Table 20.1). Aside from the cost of goods, questions have been raised regarding poor pharmacokinetic properties of these peptides, in addition to their lack of oral availability (58); however, formulation and/or chemical modification, e.g. N-methylation, of peptides may rationally improve key pharmacokinetic characteristics. Multiple N-methylation has been demonstrated to significantly improve the oral bioavailability, metabolic stability and intestinal permeability of peptides (58, 59). Advances in formulation and delivery systems, e.g. implantable scaffolds, hydrogels and microor nano- particle systems, will also help expedite the progression of immunomodulators into clinical use (60). Despite these solutions, the biggest challenge has probably been peptide in vivo stability. Development of a pegylated form of interferon-␣ for chronic hepatitis C treatment, that displays greatly enhanced stability, illustrates how technological advances in peptide derivatization can improve the clinical usefulness of biologic-based therapies (61). Another approach to increase metabolic stability is through chemically altering the peptide backbone structure, changing the traditional peptide to a so-called peptidomimetic, which can be defined as “a compound that, as the ligand of a receptor, can imitate or block the biological effect of a peptide at the receptor level” (62), or “chemical structures designed to convert the information contained in peptides into small non-peptide structures” (63). Peptidomimetics can be designed to mimic peptides and participate in protein– protein and protein–nucleic acid interactions. They often have an intrinsic ability to form stable helical conformations (64) which is important since helical motifs constitute the largest class of protein secondary structure and play a major role in mediating protein–protein interactions. At the same time these small synthetic molecules that mimic natural peptides are not susceptible to proteolytic degradation, an advantage they hold over their natural counterparts. Conversely, at the same time it can be argued that potent immunomodulatory substances should ideally be biodegradable to limit overstimulation of the immune system leading to inflammation or hyperstimulation. Thus it might be hypothesized that when moving from directly antimicrobial AMPs to host stimulatory HDPs these issues may be of lesser importance. Proteolytic degradation may in fact lead to shorter


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peptide fragments with superior immunomodulatory activity, thus eliciting responses not documented through in vitro screening. Similar phenomena have been described earlier when Domagk in the early 1930s discovered that the red textile dye Prontosil effectively inhibited streptococcal and staphylococcal infections in vivo, while being inactive against the bacteria in vitro (65). It was later concluded that a metabolic degradation product of Prontosil, a sulfanilamide, possessed the antimicrobial activity (66), illustrating one of the problems of screening for active antiinfectives in a host-free system.

6. HDPs in Clinical Development

Host defence peptides are an interesting class of agents with under-explored potential as anti-infective therapeutics. Early work explored the peptides for topical applications, exploiting their direct antimicrobial properties. Biotech companies like Magainin Pharmaceuticals (now Genaera; http://www.genaera.com), Micrologix (now Migenix; http://www.migenix.com) and IntraBiotics (http://www.intrabiotics.com) started designing therapeutic peptides that only differ from their natural homologues by a few amino acids. However, despite promising results from the early clinical trials several failed at later stages, e.g. the Genaera developed Pexiganan (MSI-78) a synthetic 22-amino-acid variant of the amphibian peptide magainin-2 (67), and the IntraBiotics Pharmaceuticals developed pig protegrin analogue Iseganan (IB-367) (68–70). Despite these disappointing early failures of cationic peptide drugs, several other new ventures have been launched, largely derived from academic labs worldwide. The first antimicrobial peptide to show statistically significant clinical effects was a bovine indolicidin homolog MX-226 (also known as Omiganan or CPI-226; originally developed by Migenix Inc, Vancouver, BC, Canada) (Table 20.1). In Phase III clinical trails, the topical application of MX-226 pentahydrochloride in a 1% gel (Omigard) led to a significant 21% reduction of colonization of central venous catheters and a 50% reduction in tunnel infections (www.migenix.com/prod 226.html) (71, 72). Intriguingly Omiganan (as CLS001) has also demonstrated efficacy as an anti-inflammatory peptide, in suppressing the effects of acute acne and Rosacea in Phase II clinical trials, confirming the multifaceted actions of these HDP derivatives. Oral candidiasis in immunocompromised patients is been tackled in a Phase IIb study by Pacgen (Vancouver, BC, Canada), using a short 12-mer peptide segment (PAC-113) originally isolated from

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human histatin 3 and 5. Much in the line of this Xoma (Berkley, CA, USA; http://www.xoma.com) is also developing a synthetic peptide from bactericidal/permeability-increasing protein, a human host defence protein. The peptide XOMA 629 has demonstrated great direct antibacterial activity and is currently undergoing clinical Phase IIa trials for topical eradication of common skin infection pathogens in addition to methicillin-resistant Staphylococcus aureus. Synthetic peptides designed based on knowledge about the immunomodulatory properties of LL-37 and other HDPs are currently being explored for their therapeutic potential (12) due to their unique ability to promote protective innate immunity while suppressing potentially harmful inflammatory responses (Fig. 20.2). A good example on the success of these studies is the described innate defence regulator-1 (IDR-1), an anti-infective peptide that selectively modulates the innate immune response (73). Optimization of immunomodulatory properties resulted in depletion of the peptides direct antibacterial properties, underlining the complex nature of the natural HDPs. However, despite lacking direct antibacterial activity, IDR-1 confers protection against multiple bacterial pathogens (i.e. methicillin-sensitive/resistant S. aureus, vancomycin-sensitive/-resistant Enterococcus and Salmonella enterica) in in vivo mice models. Studies concluded that this protection resulted from activation of monocyte-macrophage cells, stimulation of monocyte produced chemokine expression and dampening of pro-inflammatory cytokine responses (Fig. 20.2). Further optimization studies on IDR-1 has led to a 5-amino-acid peptide derivative (IMX942) that currently have been launched into preclinical development by Inimex Pharmaceuticals (Burnaby, BC, Canada) (Table 20.1). Based on the results there are plans for continuation evaluating efficacy in targeting pneumonia, surgical site infections and chemotherapy induced neutropenia. The human milk protein-derived peptide hLF1-11 was initially being developed by AM Pharma (http://www.ampharma.com) as a direct antimicrobial peptide. However, after the peptide demonstrated immunomodulatory properties the focus changed, and hLF1-11 is currently in clinical trials for evaluation of efficacy in protection and prevention of infection during allogeneic stem cell transplantation (Table 20.1). Mimicking the structural features of endogenous host defence peptides by other chemical structures has been looked upon as an attractive way to circumvent several of the drawbacks linked to peptides and peptide chemistry. One type of HDP mimics is called Ceragenins. These are synthetically produced small-molecule compounds comprised of a sterol backbone with amino acids and/or other chemical groups attached (74). Several Ceragenins have been developed by Ceragenix


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Pharmaceutical Inc. (Denver CO, USA) and have been demonstrated to possess broad-spectrum activities against multidrugresistant clinically isolated bacteria (75, 76). However, there has been unsatisfactory safety reports for cationic steroid antibiotics (77), thus restricting the use of Ceragenins to topical application or after immobilizing at the surface of medical devices for prevention of biofilms (78). Consequently Ceragenix Pharmaceutical have used their broad-spectrum antimicrobial compounds and combined it with the CerageninTM technology to formulate CeraShieldTM , antimicrobial coatings for medical devices. Preclinical studies with CeraShieldTM are currently ongoing for a variety of medical devices, from tubes and intravenous connectors to different catheters and orthopaedic and surgical implants (http://www.ceragenix.com/). Another class of mimetic has been developed by PolyMedix Inc. (Radnor, PA, USA). PolyMedix has tailored small chemical molecules that mimic several of the well HDPs. On example from their portfolio is a peptide mimetic whose design was based on the structure of the well-described HDP magainin. This mimetic mPE (meta-phenylene ethynylene) has demonstrated activity against a variety of bacterial and Candida species down to nano-molar concentrations (79). Another of their compounds, a small non-peptide mimetic (PMX-30063), mimics the amphiphilic structure of defensines. PMX-30063 is claimed to be bactericidal against both Gram-positive and Gram-negative bacteria by disruption of the bacterial cell membrane, and the company has also other small molecule mimetic that possess similar activities (80). PMX-30063 has demonstrated efficacy in a mice model of systemic S. aureus infection at 2 mg/kg, and a Phase I clinical safety study with PMX-30063 has just been completed, demonstrating a safe and well-tolerated single doses with no observable adverse effects up to 24 mg/kg per day (Press release).

7. Conclusion We are entering the “post-antibiotic era” in which many previously successful drug regimes are becoming ineffective, consequently the time has come to vigorously pursue alternative potential treatment approaches toward infectious diseases. Development of HDPs as immunomodulatory therapeutic alternatives is questionably subject to unique difficulties. The innate immune system is intrinsically complex and there is great genetic variation between individuals; additionally there is fundamental interspecies differences (81) cluttering the correlation between animal models and human trials. However, the complexity of the

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innate immune system through its evolution has also resulted in huge redundancy, thus almost duplicating critical response cascades, hence creating a safety net for drug developers while also undermining the effectiveness of single targeting drug candidates. The success of peptides as drugs, and especially HDPs as antiinfectives, has not carried significant fruits yet. However, this concept is in its infancy and with continued research and adaptation of new technology platforms especially introducing bioinformatics approaches, it may enable this strategy to solve some of the forthcoming challenges we will be facing from emerging infections diseases. Any disease is per definition caused by a pathogen’s ability to overcome or circumvent the host immune response, thus we argue that development of novel anti-infectives directly targeting the host immune system has a reasonable chance of succeeding, while a reduced chance of resistance development.

Acknowledgments This manuscript is dedicated to the memory of Aaron W.J. Wyatt who tragically passed away on 24 December 2008. Aaron was not only a superb colleague but also a good friend. The author’s research in this area was supported by the Foundation for the National Institutes of Health, Gates Foundation and Canadian Institutes for Health Research through two separate Grand Challenges in Global Health Initiatives and by Genome British Columbia for the Pathogenomics of Innate Immunity Research Program. REWH is the recipient of a Canada Research Chair. References 1. Hamill, P., Brown, K., Jenssen, H., and Hancock, R. E. W. (2008) Novel anti-infectives: is host defence the answer?. Curr. Opin. Biotechnol. 19, 628–636. 2. Lai, Y. and Gallo, R. L. (2008) Toll-like receptors in skin infections and inflammatory diseases. Infect. Disord. Drug Targets 8, 144–155. 3. O’Neill, L. A. (2006) Targeting signal transduction as a strategy to treat inflammatory diseases. Nat. Rev. Drug Discov. 5, 549–563. 4. Kanzler, H., Barrat, F. J., Hessel, E. M., and Coffman, R. L. (2007) Therapeutic targeting of innate immunity with Toll-like receptor agonists and antagonists. Nat. Med. 13, 552–559.

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73. Scott, M. G., Dullaghan, E., Mookherjee, N., Glavas, N., Waldbrook, M., Thompson, A., Wang, A., Lee, K., Doria, S., Hamill, P., Yu, J. J., Li, Y., Donini, O., Guarna, M. M., Finlay, B. B., North, J. R., and Hancock, R. E. W. (2007) An anti-infective peptide that selectively modulates the innate immune response. Nat. Biotechnol. 25, 465–472. 74. Lai, X. Z., Feng, Y., Pollard, J., Chin, J. N., Rybak, M. J., Bucki, R., Epand, R. F., Epand, R. M., and Savage, P. B. (2008) Ceragenins: cholic acid-based mimics of antimicrobial peptides. Acc. Chem. Res. 41, 1233– 1240. 75. Chin, J. N., Rybak, M. J., Cheung, C. M., and Savage, P. B. (2007) Antimicrobial activities of ceragenins against clinical isolates of resistant Staphylococcus aureus. Antimicrob. Agents Chemother. 51, 1268–1273. 76. Van Bambeke, F., Mingeot-Leclercq, M. P., Struelens, M. J., and Tulkens, P. M. (2008) The bacterial envelope as a target for novel anti-MRSA antibiotics. Trends Pharmacol. Sci. 29, 124–134. 77. Savage, P. B., Li, C., Taotafa, U., Ding, B., and Guan, Q. (2002) Antibacterial properties of cationic steroid antibiotics. FEMS Microbiol. Lett. 217, 1–7. 78. Savage, P. B., Pollard, J., Feng, Y., Reddy, L. K., and Genberg, C. (2008): Use of a Ceragenin-Based Coating to Prevent Bacterial Colonization of Urinary Catheters. In Interscience Conference on Antimicrobial Agents & Chemotherapy pp. Poster K–1479. 79. Beckloff, N., Laube, D., Castro, T., Furgang, D., Park, S., Perlin, D., Clements, D., Tang, H., Scott, R. W., Tew, G. N., and Diamond, G. (2007) Activity of an antimicrobial peptide mimetic against planktonic and biofilm cultures of oral pathogens. Antimicrob. Agents Chemother. 51, 4125–4132. 80. Scott, R. W., DeGrado, W. F., and Tew, G. N. (2008) De novo designed synthetic mimics of antimicrobial peptides. Curr. Opin. Biotechnol. 19, 620–627. 81. Viola, A. and Luster, A. D. (2008) Chemokines and their receptors: drug targets in immunity and inflammation. Annu. Rev. Pharmacol. Toxicol 48, 171–197. 82. Sawai, M. V., Jia, H. P., Liu, L., Aseyev, V., Wiencek, J. M., McCray, P. B., Jr., Ganz, T., Kearney, W. R., and Tack, B. F. (2001) The NMR structure of human beta-defensin2 reveals a novel alpha-helical segment. Biochemistry 40, 3810–3816. 83. Mandard, N., Sodano, P., Labbe, H., Bonmatin, J. M., Bulet, P., Hetru, C., Ptak, M., and Vovelle, F. (1998) Solution structure of thanatin, a potent bactericidal and fungici-

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Chapter 21 Assay Systems for Measurement of Anti-inflammatory Activity Evelina Rubinchik and Christopher Pasetka Abstract It is widely accepted that cationic antimicrobial peptides possess potent microbicidal properties. Recent studies show that in addition to their antimicrobial action, these peptides can exhibit anti-inflammatory activity. The purpose of this chapter is to describe in vivo ear inflammation models that can be used for evaluating the anti-inflammatory activity of antimicrobial peptides. The models are based on different mechanisms of inflammation development and include irritant dermatitis (a model induced by a single application of 12-o-tetradecanoylphorbol acetate [TPA]) and allergic dermatitis, or delayed type hypersensitivity reaction (a model induced by repetitive application of oxazolone). Key words: Antimicrobial peptides, irritant dermatitis model, allergic dermatitis model, TPA, oxazolone.

1. Introduction It is widely accepted that cationic antimicrobial peptides possess potent microbicidal properties. Recent studies show that in addition to their antimicrobial action, these peptides can exhibit anti-inflammatory activity. For example, in vitro, antimicrobial peptides were shown to regulate genes associated with antiinflammatory or pro-inflammatory mediators (1, 2) and reduce cytokine production (3–5). In vivo, the anti-inflammatory activity was also demonstrated in murine models of ear inflammation induced by TPA (6, 7) and oxazolone (7). The purpose of this chapter is to describe two simple and reliable in vivo inflammation models that can be used for A. Giuliani, A.C. Rinaldi (eds.), Antimicrobial Peptides, Methods in Molecular Biology 618, DOI 10.1007/978-1-60761-594-1 21, © Springer Science+Business Media, LLC 2010

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evaluating the anti-inflammatory activity of antimicrobial peptides. The first model is TPA-induced acute ear edema which is a model of irritant dermatitis (8). The mechanism by which TPA causes inflammation is related to increased vascular permeability mediated by the release of prostaglandins, leukotrienes, histamine, and serotonin (9). The main advantage of the TPA model is that it is fast, relatively easy to perform, and well characterized. One of the disadvantages is that inflammation develops very rapidly, thus only prophylactic treatment can be evaluated. Another disadvantage is that the model is known to generate false-positive results as agents that are not recognized as anti-inflammatory compounds in humans have shown activity in it (10). Therefore, the use of secondary models should be considered. One of the more popular models used is ear inflammation induced by oxazolone, which is an example of an allergic dermatitis model (9). The mechanism of action is a delayed hypersensitivity reaction that requires mice to be first sensitized by application of oxazolone and then challenged several days later by a second application of oxazolone. This second application results in the development of an inflammatory response.

2. Materials 2.1. Irritant Dermatitis Model

1. 95% ethanol, USP (Sigma). Store at room temperature. 2. 12-o-tetradecanoylphorbol acetate (TPA), (Sigma). Store at –20◦ C. 3. Dimethyl sulfoxide (DMSO), (Sigma). Store at room temperature. 4. Dexamethasone (Sigma). Store at 2–8◦ C. 5. Acetone (Sigma). Store at room temperature. 6. Stock TPA solution: 0.5% (w/v) TPA solution in DMSO (prepare in a glass vial). Distribute into 100–200 ␮L aliquots and store at –20◦ C for up to 6 months. 7. Final TPA solution (see Note 1): 0.005% TPA solution in acetone prepared by diluting 1 volume of the stock 0.5% TPA solution with 99 volumes of acetone (see Note 2). Keep at room temperature and use within 2 h of preparation. 8. Peptide solutions: dissolve the peptide to the desired concentrations (typically in the 0.1–5.0% (w/v) range) in 95% ethanol (see Note 3). Keep protected from light at room temperature and use on the day of preparation (unless stability is characterized and supports longer storage).

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9. Positive control (dexamethasone) solution: 0.1% (w/v) dexamethasone solution in 95% ethanol. 2.2. Allergic Dermatitis Model

1. 4-Ethoxymethylene-2-phenyloxazone (oxazolone) (Sigma). Store at 2–8◦ C. 2. Acetone (Sigma). Store at room temperature. 3. Corn oil (Sigma). Store at room temperature. 4. 95% Ethanol, USP grade (Sigma). Store at room temperature. 5. Oxazolone induction solution: 3% (w/v) oxazolone solution prepared in a 5:1 (v/v) mixture of acetone:corn oil carrier. Use within 2 h of preparation (see Note 2). 6. Oxazolone challenge solution (see Note 4): 1% (w/v) oxazolone solution in acetone. Use within 2 h of preparation (see Note 2). 7. Peptide solutions: refer to Step 8 of Section 2.1. 8. Positive control (dexamethasone) solution: refer to Step 9 of Section 2.1.

2.3. Animals

CD-1 female mice that are 5–6 weeks of age (21–27 g) are used in these studies. All animals have free access to a standard certified pelleted diet and water.

2.4. Supplies

1. 8-mm dermal biopsy punch (Miltex Instrument Company, Inc.). 2. 2 or 4 mL glass vials (made of low extractable borosilicate glass) with screw-up caps (Wheaton, VWR). 3. 1.7 mL polypropylene microcentrifuge tubes, pre-weighed (VWR or Fisher Scientific).

3. Methods 3.1. Irritant Dermatitis Model

1. One day before the start of the experiment weigh the animals and evaluate their health status. Any animals in poor health or out of the specified weight range should not be assigned to experimental groups and must be replaced by spare animals obtained from the same batch and maintained under the same environmental conditions. 2. Randomize the animals into groups of 5–10 mice making sure that each group has the same mean body weight and house each group in a separate cage(s) labeled with the group identification.

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3. To induce ear inflammation, apply a 20 ␮L volume of 0.005% (w/v) TPA solution as a single topical application on the dorsal area of the right ear of each animal using a 20 ␮L pipette. Spread the volume evenly over the whole surface of the ear. 4. Apply 20 ␮L of the peptide or dexamethasone (positive control) solutions topically to the dorsal area of the right ear immediately after TPA application (see Notes 5 and 6). Spread the volume evenly over the whole surface of the ear. Treat the animals in the vehicle control group with 20 ␮L of 95% ethanol. 5. Leave the left ears untreated (no TPA or treatment applications) to serve as background controls. 6. At 6.0 h ± 10 min after administration of TPA, euthanize mice by CO2 asphyxiation. Remove both the left and right ears and obtain an 8-mm biopsy from each ear using a dermal biopsy punch. Ensure that the biopsies are removed from the exact same area of the ear in all animals. 7. Place the biopsy into a pre-weighed microcentrifuge tube (see Note 7) labeled with the animal identification number and ear site (left or right). Determine biopsy weights and analyze results as described in Section 3.3. below. 3.2. Allergic Dermatitis Model

1. Evaluate and randomize the animals as described in Steps 1 and 2 of Section 3.1. 2. Clip the fur from each animal’s abdomen the day before the experiment is to start, taking care not to abrade the skin. 3. On the day of the experiment (day 0), apply a 50 ␮L volume of 3% oxazolone induction solution to all mice as a single topical application on the shaved abdomen using an appropriately sized pipette. Spread the volume evenly over the application area. 4. On day 5, apply a 20 ␮L volume of 1% oxazolone challenge solution (see Note 4) as a single topical application on the dorsal area of the right ear using a 20 ␮L pipette. Spread the solution evenly over the whole surface of the ear. 5. One hour after the oxazolone challenge, apply 20 ␮L of the peptide solution, vehicle control or positive control (dexamethasone) solution topically to the dorsal area of the right ear (see Notes 5 and 6). Spread the volume evenly over the whole surface of the ear. The animals in the vehicle control group will receive 20 ␮L of the vehicle. 6. At 24 h ± 10 min after application of oxazolone, euthanize the animals by CO2 asphyxiation. Remove both left and right ears and obtain 8-mm biopsies from each ear making


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sure that the biopsies are collected from the exact same area of the ear in all animals. 7. Place the biopsy into a pre-weighed microcentrifuge tube (see Note 7) labeled with the animal number and biopsy location (left or right ear). Determine the biopsy weights and analyze the results as described in Section 3.3. 3.3. Data Analysis

1. Calculate the difference in biopsy weights between the right (treated) and left (untreated) ears and determine the percent of ear weight increase according to the formula: [Right ear weight (mg) − Left ear weight (mg)] × 100% Left ear weight (mg) 2. Present the data as mean ± standard deviation and perform a statistical analysis to compare biopsy data from the treated group with the vehicle control group.

3.4. Study Design and Experimental Strategy

1. It is a good idea to perform a model development study before the initiation of drug testing to ensure that the optimal concentrations of TPA and oxazolone are used (see Notes 1 and 4). 2. Use 5–6 animals per group in the exploratory studies (e.g., dose range-finding experiments) and 10 animals per group in the definitive studies as, even with the best techniques, the results can be variable. 3. Ensure that the drug effect is determined by comparing to the response in the vehicle-treated group and not to the untreated group as some formulation excipients may also exhibit inhibitory activity, especially in the TPA model (see Note 3). It is also a good idea to determine the vehicle effect in a preliminary experiment to ensure that it has a minimal or no effect on inflammation. 4. We also recommend testing activity of the peptide alone to ensure that it does not cause irritation on its own when used at high concentrations (see example in Step 5 of Section 3.4 below). 5. An example of the evaluation of the anti-inflammatory activity of an antimicrobial peptide in the TPA and oxazolone models is shown in Fig. 21.1. The peptide 11J68CN is a novel, synthetic, antimicrobial peptide (indolicidin analog) comprised of 13 amino acid residues with the following primary sequence: W (Dab) W W (Dab) P (Dab) W (Dab) W P (Dab) W-amide, where W=tryptophan, Dab=2,4-diamino butyric acid, and P=proline. The peptide has demonstrated in vitro activity against a wide variety of Gram-positive and Gram-negative bacteria and fungi

354


a

b TPA model

80 60 *

40

**

20

% increase of ear biopsy weight


Oxazolone model

200

100

150 **

100 50 0

0 0% (vehicle)

1%

0% (vehicle) 0.1% 1% peptide concentration

5%

peptide concentration

5%

c


100

Background irritation

75 50 25 0 –25

0% (vehicle) 0.1%

1%

5%

peptide concentration

Fig. 21.1. Evaluation of anti-inflammatory activity of antimicrobial peptide 11J68CN. The peptide reduces ear edema induced by TPA (a) and oxazolone (b) and does not cause irritation when used alone (c). ∗ – P < 0.05, ∗∗ – P < 0.001.

(11). In vivo, the peptide inhibited, in a dose-dependent manner, TPA-induced inflammation (up to 85% inhibition, Fig. 21.1a) and oxazolone-induced inflammation (up to 49% inhibition, Fig. 21.1b). In addition, the effect of peptide alone was evaluated with the results indicating that the peptide was not an irritant (application of vehicle or peptide solutions resulted in insignificant (±15%) changes in the ear biopsy weights, Fig. 21.1c).

4. Notes 1. Before starting peptide testing, we recommend confirming in a preliminary experiment that the 0.005% TPA concentration results in an optimal inflammatory response


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as differences between mouse breeds and treatment application techniques may affect the outcome of edema development. The goal of such a preliminary experiment is to determine the TPA concentration that results in significant but manageable ear inflammation. A very high TPA dose may result in irreversible damage and ear necrosis (12). An example of such an experiment is shown in Fig. 21.2. In this study, a 20 ␮L volume of the vehicle solution (acetone) or 0.0005, 0.005, and 0.05% TPA solution was applied to separate groups of mice. Three mice from each group were sampled at 1, 3, 6, and 24 h after TPA administration. The results (Fig. 21.2) indicate that the 0.0005% TPA concentration was too low to induce inflammation, while the 0.05% TPA solution resulted in inflammation that was too significant (i.e., persisted for more than 24 h). In contrast, the 0.005% TPA solution appeared to be an optimal concentration as it produced considerable but controllable inflammation. 2. Acetone is a highly volatile vehicle that, if left in an open container, may evaporate to a significant degree thus increasing the concentration of the agent dissolved in it. For preparation of TPA and oxazolone solutions in acetone, use a glass vial with a tightly closing cap and a volume that is equal to or just slightly greater than the final solution volume. The vial must be kept tightly closed between applications in order to prevent evaporation of the acetone.


3. Ethanol is a typical vehicle of choice for treatment formulations as it helps with drug solubility and also enhances skin penetration. Moreover, ethanol alone has no significant effect on TPA- and oxazolone-induced ear inflammation. If other vehicles are to be used, their effect on inflammatory response must be determined in a preliminary experiment since high activities may be observed with some

140

0% TPA (control)

120

0.0005% TPA

100

0.005% TPA 0.05% TPA

80 60 40 20 0 0

5

10

15

20

25

hours

Fig. 21.2. Ear edema development induced by various concentrations of TPA.


formulations. Such vehicles must be avoided and alternative formulations should be used to ensure that a true drug effect is determined. The TPA model is especially sensitive with significant non-specific inhibitory responses occasionally observed. 4. Similarly to the TPA model, it is important to determine the optimal oxazolone concentration in a preliminary experiment. The goal of such a preliminary experiment is to determine the oxazolone concentration that results in significant ear inflammation but is not accompanied by the direct irritation that can be observed at high oxazolone concentrations. An example of such an experiment is shown in Fig. 21.3. In this study, the animals were induced with a 3% oxazolone solution and challenged with either 0.25, 0.5, 1, or 2% oxazolone solutions. A separate group of mice was induced with 0% oxazolone (vehicle only) and challenged with 0.25–2% oxazolone solutions to monitor for direct irritation. The effect was evaluated at 24 h post challenge. The results (Fig. 21.3) indicate that 1% oxazolone induced a significant inflammatory effect without being a direct irritant while irritation was observed with 2% oxazolone. 5. Peptide treatments can be applied at times that differ from those indicated in the methods above. In addition, peptides can be formulated in vehicles different from those recommended above. The following information should be taken into consideration when making a decision on the timing of treatment application and the type of formulation to be

challenge only induction and challenge 180 160 % increase of ear biopsy weight

356

140 120 100 80 60 40 20 0 0.25%

0.5%

1.0%

2.0%

Oxazolone concentration at challenge phase

Fig. 21.3. Ear edema development induced by various concentrations of oxazolone at challenge stage.


357

used. The inflammatory reaction in the TPA model develops very rapidly, thus the treatments should be administered either immediately after (most typical approach) or no later than 15–30 min post induction. Such a rapid inflammatory response also requires rapid penetration of the applied treatment. In order to ensure significant skin penetration, the treatments are typically formulated in vehicles that enhance skin penetration such as acetone or ethanol. We recommend avoiding acetone since it is a more volatile vehicle than ethanol. Since inflammation takes longer to develop in the oxazolone model, a delay in the treatment application is possible. We usually apply treatment at 1 h post oxazolone application but we also employed treatments at 3 and/or 5 h post challenge. Regarding formulation, both pure solvents (usually 95% ethanol) and complex topical formulations can be employed. 6. Treatment with 0.1% (w/v) dexamethasone serves as a positive control and is expected to result in significant inhibition of TPA- and oxazolone-induced ear edema. In our hands, we typically observed a statistically significant inhibition of ≥90% for the TPA model and 60–90% for the oxazolone model. If dexamethasone does not show a significant inhibitory effect, this usually indicates that the inflammation is too severe to be abrogated and the model conditions should be adjusted. 7. The weight of ear biopsies may be affected by the leakage of the extracellular exudate from the inflamed tissues. Our preliminary experiments indicate that while control (untreated) biopsy weights remain stable over 2 h, the biopsies from inflamed tissues lose up to 9% of their weight. Therefore, we recommend placing biopsies in pre-weighed eppendorf tubes immediately after collection and weighing them together with any exudate to ensure accurate measurements. References 1. Scott, M. G., Rosenberger, C. M., Gold, M. R., Finlay, B. B., and Hancock, R. E. (2000) An alpha-helical cationic peptide selectively modulates macrophage responses to lipopolysaccharide and directly alters macrophage gene expression. J. Immunol. 165, 3358–3365. 2. Scott, M. G., Davidson, D. J., Gold, M. R., Bowdish, D., and Hancock, R. E. (2002) The human antimicrobial peptide LL-37 is a multifunctional modulator of innate immune responses. J. Immunol. 169, 3883–3891.

3. McInturff, J. E., Wang, S. J., Machleidt, T., Lin, T. R., Oren, A., Hertz, C. J., Krutzik, S. R., Hart, S., Zeh, K., Anderson, D. H., Gallo, R. L., Modlin, R. L., and Kim, J. (2005) Granulysin-derived peptides demonstrate antimicrobial and anti-inflammatory effects against Propionibacterium acnes. J. Invest. Dermatol. 125, 256–263. 4. Masera, R. G., Bateman, A., Muscettola, M., Solomon, S., and Angeli, A. (1996) Corticostatins/defensins inhibit in vitro NK activity and cytokine production by human

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5.

6.

7.

8.

Rubinchik and Pasetka peripheral blood mononuclear cells. Regul. Pept. 62, 13–21. Guarna, M. M., Coulson, R., and Rubinchik, E. (2006) Anti-inflammatory activity of cationic peptides: application to the treatment of acne vulgaris. FEMS Microbiol. Lett. 257, 1–6. Scott, M. G., Lee, K., Maclean, S., Gong, J., Finlay, B. B., and Hancock, R. E. W. (2003) Immunomodulatory peptides that protect in murine models of infection. Abstr 43rd Intersci. Conf. Antimicrob. Agents Chemother. 43, 62. McNicol, P. J., Rubinchik, E., Pasetka, C., Barger, R., Lopez, J., and Friedland, H. D. (2001) MBI 594AN is active against Acne vulgaris organisms, does not induce resistance and has anti-inflammatory activity in vivo. Abstr 41st Intersci. Conf. Antimicrob. Agents Chemother. 41, 205. Rao, T. S., Currie, J. L., Shaffer, A. F., and Isakson, P. C. (1993) Comparative evaluation

9.

10.

11.

12.

of arachidonic acid (AA)- and tetradecanoylphorbol acetate (TPA)-induced dermal inflammation Inflammation 17, 723–741. Tramposch, K. M. (1999) Skin inflammation. In In vivo models of inflammation. Morgan, D. W., Marshall, L. A. (Eds.), pp. 179–204. Basel, Switzerland: Birkhauser Verlag. Carlson R. P., O’Neill-Davis, L., Chang, J., and Lewis, A. J. (1985) Modulation of mouse ear edema by cyclooxygenase and lipoxygenase inhibitors and other pharmacologic agents Agents Actions 17, 197–204. Krieger, T. J., and McNicol, P. J. (2004) Antimicrobial cationic peptides and formulations thereof. Patent number US 6,835, 536 B2. Young, J. M., Wagner, B. M., and Spires, D. A. (1983) Tachyphylaxis in 12-otetradecanoylphorbol acetate- and arachidonic acid-induced ear edema J. Invest. Dermatol. 80, 48–52.

Chapter 22 Ex Vivo Skin Infection Model Evelina Rubinchik and Christopher Pasetka Abstract Over the past decade, the emergence of bacterial strains resistant to conventional antibiotics has necessitated the discovery and development of new antimicrobial therapies. This chapter describes a skin infection model that is based on the use of excised skin derived from the domestic pig. The model conditions mimic the environment of human skin and efficiently support the growth of clinically relevant bacterial and fungal species, thus making it useful for evaluating the activity of antimicrobial peptides and other antibiotics as well as their respective formulations. Key words: Antimicrobial peptides, skin infection model, Gram-positive bacteria, Gram-negative bacteria, fungi.

1. Introduction Several different in vivo skin infection models have been described in the literature (1–3); however, none have entered into widespread use. It is well known that the skin of rodents, i.e., species typically employed in such studies, differs significantly from human skin and offers a poor support for the growth of clinically relevant human pathogens. Treatment applications are also challenging and require occlusion to prevent animals from licking and grooming the infected site. The purpose of this chapter is to describe a simple and reliable ex vivo skin infection model that significantly reduces the use of experimental animals while allowing for the simple and reproducible evaluation of a compound’s antimicrobial activity. The model is based on the use of excised skin derived from the domestic pig. The skin pieces are disinfected and inoculated with


359

360


human pathogens. The treatment is then applied and the number of colony forming units (CFU) per skin piece is determined after incubation. This model provides several advantages. First, the morphological and functional characteristics of pig skin are comparable to those of human skin (4). Second, large quantities of pig skin can be easily obtained and kept frozen for long periods of time, thus allowing for flexibility in experiment initiation. Third, the skin can be inoculated with various human pathogens under conditions (temperature, humidity) that mimic human skin colonization and promote organism survival and growth. Finally, the model allows for accurate quantitative determination of the antimicrobial or antifungal activity of both antimicrobial peptides and their topical formulations.

2. Materials 2.1. Pig Skin

Pig skin obtained from female or male domestic pigs (see Note 1).

2.2. Microorganisms

Gram-positive and Gram-negative bacteria and fungi obtained from ATCC (methicillin-sensitive Staphylococcus aureus ATCC 14154; Escherichia coli ATCC 25922; Enterobacter cloacae ATCC 13047; Serratia marcescens ATCC 13880, Candida albicans ATCC 14053) or from clinical laboratories (methicillin-resistant S. aureus, S. epidermidis, and Propionibacterium acnes). The organisms listed above were successfully used in this model in our laboratory but other organisms and/or strains can also be employed. Store vials with bacterial and fungal cultures at –70◦ C. Do not thaw.

2.3. Microbiology Supplies

Microbiology supplies can be purchased from any general scientific supply company such as Sigma, Fisher, or VWR. 1. 5% sheep blood agar plates; trypticase soy agar (TSA) plates for culture of S. aureus, S. epidermidis, S. marcescens, and C. albicans; McConkey agar plates for culture of E. coli and E. cloacae; Wilkins–Chalgren agar plates for culture of P. acnes. Store plates inverted at 4◦ C (see Notes 2 and 3). 2. Sterile Petri plates (15 × 100 mm, polystyrene). 3. Inoculating loops (sterile, single-use plastic loops or reusable metal loop). 4. Bacterial cell spreaders (25.4 mm spreader head, metal). 5. Inoculating turntable. 6. 0.5 McFarland turbidity standard (16 × 125 mm glass tube). Store at 2–30◦ C, protected from light.

Ex Vivo Skin Infection Model

361

7. Sterile cotton swabs (152.4 mm, wood). 8. Glass culture tubes (16 × 125 mm, borosilicate glass). 9. Plastic tubes (12 × 75 mm, 5 mL, snap-cap, polystyrene). R kit with catalyst (BBL Gas-Pak 10. Anaerobic jar and Gas Pak system).

2.4. Reagents

1. 70% ethanol, denatured (VWR). Store at room temperature. 2. NaCl. Store at room temperature. 3. Isotonic saline solution: 0.9% NaCl solution in Milli-Q or deionized water. Sterilize by filtration through 0.2 ␮m filter. Store at room temperature for up to 1 month. 4. Polyanetholesulfonic acid (PSA), (Sigma). Store at room temperature. 5. PSA solution: 1% (w/v) PSA solution in isotonic saline. Sterilize by filtration through 0.2 ␮m filter. Prepare the solution fresh on the day of the experiment. 6. Peptide formulations: dissolve the peptides to the desired concentration (typically in the 0.1–5.0% (w/v) range) in 0.9% saline. Adjust pH to 4–8 to avoid extreme values. Keep protected from light at room temperature and use on the day of preparation (unless stability is characterized and supports longer storage). In addition to saline, more complex formulations such as creams, gels, or ointments can be employed, allowing for a more accurate simulation of the treatment conditions in the clinical setting.

3. Methods 3.1. Preparation of Pig Skin Samples

1. Immediately after animal sacrifice, clip the pig skin free of hair and swab thoroughly with 70% ethanol (see Note 4). 2. Surgically remove the required number of skin sections (approximately 20 × 20 cm each). Store the sections at –20◦ C in re-sealable plastic bags, pre-swabbed with 70% ethanol. Expel the air from the bags to reduce skin dehydration. 3. On the day of the experiment, remove any remaining fat layers from the frozen skin sections with a scalpel and cut the skin into 2 × 2 cm pieces using a sterile metal ruler as a measuring guide. 4. Sterilize the thawed skin pieces by immersing them in 70% alcohol (see Note 4).

362


5. Pat dry the skin pieces with sterile (autoclaved) paper towels and distribute into experimental groups. Place the pieces from the same treatment group into sterile Petri plates (up to 5 pieces/plate) labeled with group identification numbers (see Note 5). 3.2. Preparation of Bacterial Inoculum

1. For plate inoculation, use either disposable plastic loops or a reusable metal inoculating loop. If a metal loop is used, sterilize it by holding it in a gas or ethanol burner flame until it is red hot. Cool the metal loop by touching it to a sterile portion on the surface of an agar plate until it stops sizzling. 2. Remove the tube with the frozen bacterial or fungal culture from the freezer, open the cap, and scrape the frozen surface with the inoculation loop. Do not allow the contents of the vial to thaw. 3. Streak bacteria or fungi across one third of a 5% sheep blood agar plate. Using a new plastic loop or sterilized metal loop, pass the loop through the first streak and streak across a new third of the plate. Repeat one more time to inoculate the remaining third of the plate. 4. Incubate the plates (inoculated surface facing down) with aerobic organisms (e.g., S. aureus) for 24–48 h at 35±2◦ C or until colonies become visible. Incubate the plates with anaerobic organisms (e.g., P. acnes) for 48–72 h at 35±2◦ C in an anaerobic environment i.e., in a securely closed anaerR obic jar with a Gas Pak CO2 generator. Ensure that a palladium catalyst has been attached to the underside of the anaerobic jar lid prior to sealing to remove residual oxygen. 5. At the end of the incubation period, examine the plate to ensure that no contaminating colonies are present. Collect several isolated colonies using a sterile inoculation loop, suspend them in 5 mL of sterile saline in a sterile glass culture tube, and vortex well. 6. Adjust the concentration of the suspension to 108 colony forming units (CFU) per mL by comparing the turbidity to that of a 0.5 McFarland standard (see Note 6). Ensure that both the McFarland standard and bacterial or fungal suspensions are well suspended prior to visual comparison. 7. Dilute the bacterial or fungal suspension with sterile saline to obtain a final inoculum of 103 –107 CFU/mL (see Note 7) and use this inoculum immediately after preparation to infect the skin pieces as described in Section 3.3. 8. Verify the concentration of the final inoculum by preparing one-log (10-fold) serial dilutions of the inoculum. The pro-


363

cedure described below is based on a 107 CFU/mL final inoculum size but it can be easily adjusted for other inoculum sizes. The dilutions of the final inoculum are prepared by mixing 100 ␮L of the 107 CFU/mL bacterial or fungal suspension into 900 ␮L of sterile saline (10–1 dilution). Following vortexing, a 100 ␮L aliquot of the 10–1 dilution is transferred into 900 ␮L of sterile saline to yield a 10–2 dilution. The process is repeated until dilutions ranging from 10–1 to 10–5 have been prepared. Ensure that each suspension is mixed well by vortexing immediately prior to the removal of an aliquot for dilution. 9. Pipet 100 ␮L of each dilution onto a dry, pre-labeled agar plate. Sterilize a metal spreader by dipping the triangular portion into a container with 70% ethanol and passing it through a burner flame to ignite the ethanol and allowing the flame to burn out. Cool the spreader by touching it to the surface of an agar plate (without bacterial cells). With the inoculated plate on the turntable, spin the turntable and spread the 100 ␮L bacterial aliquot over the entire agar surface. 10. After application, allow plates to dry and then incubate as described in Step 4 of Section 3.2. During incubation, each bacterial cell will grow into a separate CFU. 11. Determine the final inoculum size from the number of CFUs observed on the diluted plates. Specifically, select the plates that show 10 to 200 well-separated colonies per plate and count all colonies on the plate. This is the number of live organisms that is present in a 100 ␮L aliquot. By multiplying this number by 10, the number of CFUs per 1 mL can be determined. This CFU/mL value is then multiplied by the corresponding dilution factor to determine the final inoculum concentration. For example, if 12 colonies were observed on the plate corresponding to the 10–5 -fold dilution, then the number of bacteria in 1 mL of the final inoculum (undiluted) is 12 × 10 × 105 = 1.2 × 107 CFU/mL. 3.3. Skin Inoculation and Treatment

1. Perform all procedures under aseptic conditions. Following distribution of the skin pieces into each treatment group (described in Step 5 of Section 3.1 ), apply a 50 ␮L aliquot of the bacterial inoculum (103 –107 CFU/mL, see Note 7) to the dry epidermal side of the skin and spread uniformly over the entire area using a sterile pipet tip. 2. Replace the plate lid and incubate the plate with inoculated skin pieces at 35±2◦ C in a humidified chamber (i.e., a plastic container humidified by placing paper towels soaked in water

364


on the bottom) until the time of treatment initiation. For P. acnes, perform the incubation under anaerobic conditions. 3. Depending on the goal of the experiment, the treatment can be initiated either immediately or with a 1–8 h delay postinoculation. We recommend delaying the treatment initiation (e.g., for 2 h) to allow the bacteria to establish an infection. 4. Apply 25–100 ␮L of the peptide formulation onto the infected side of each skin piece and spread uniformly over the entire area using a sterile pipet tip (see Notes 8 and 9) 5. Treat the samples from the vehicle group with an identical volume (25–100 ␮L) of the vehicle formulation. Leave the skin pieces from the control group without treatment. 6. Incubate the Petri plates containing the skin pieces in a humidified chamber for up to 24 h at 35±2◦ C. For P. acnes, perform the incubation under anaerobic conditions. 3.4. Determination of Bacterial Counts

1. Following the desired incubation period (1–24 h), remove the skin samples from the humidified chamber. 2. Label sterile tubes with sample identification numbers and add 1 mL of sampling solution (0.9% NaCl supplemented with 1% PSA). Other concentrations of PSA can be selected as described in Section 3.5. 3. To collect bacteria or fungi from a skin piece, dip a sterile cotton swab into 1 mL of sampling solution and swab the pig skin surface 5–10 times, making sure that the whole area is covered by swabbing. Repeat the swabbing procedure three times in total. 4. After the final swab, vortex the tube holding the cotton tip in the solution. Squeeze the solution out of the cotton tip into the sampling tube and discard the swab. 5. Prepare one-log (10-fold) serial dilutions of the sampling solution in 0.9% saline as described in Step 8 of Section 3.2. 6. Plate 100 ␮L of each dilution onto a pre-labeled agar plate as described in Steps 9 and 10 of Section 3.2 (see Note 10). 7. Incubate the plates at 35±2◦ C for 24 h (or until colonies are clearly visible). Incubate plates inoculated with P. acnes for 48 to 72 h at 35±2◦ C in an anaerobic environment. Quantify the number of CFUs as described in Step 11 of Section 3.2. Assign the low level of detection value (10 CFU/site) to a sample in the event that no viable colonies are detected on the plates. 8. Calculate the CFUs and log10 CFU/skin piece and determine log10 CFU/site ± standard deviation (SD) for each group.


3.5. Inhibition of Residual Antimicrobial Activity

365

When performing swabbing of the skin to collect bacteria, the antimicrobial peptide may also be transferred into the sampling solution. This could result in false-positive activity because of a peptide carry-over effect (not associated with activity on the skin surface). Therefore, any residual antimicrobial activity must be abrogated by the addition of an appropriate inhibitor to the sampling solution (5). The selection of inhibitor for antimicrobial peptides is based on the fact that they are cationic and will therefore interact with negatively charged molecules (e.g., PSA) resulting in precipitation, rendering the peptide inactive. 1. Apply the antimicrobial peptide (at the highest concentration to be used in the study) to 12 pig skin pieces as described in Step 4 of Section 3.3 and incubate for the desired amount of time. 2. At the end of incubation, swab skin pieces into 1 mL of sterile saline containing different concentrations of the selected inhibitor (e.g., 0.01, 0.1, and 1% (w/v) PSA). Use three skin pieces per group. Swab the remaining three pieces into saline without inhibitor. 3. Prepare a bacterial or fungal lawn by spreading 100 ␮L of a 107 –108 CFU/mL inoculum over the agar plate (employ the organism that you intend to use in your experiments). Allow plates to dry. 4. Apply a 10–20 ␮L aliquot of the swabbed sampling solutions (peptide + inhibitor) onto the bacterial lawn at the pre-labeled sites of the plate. In addition, apply the peptide solution without inhibitor and the inhibitor solution without the peptide. 5. Incubate the plate for 18–24 h at 35±2◦ C and examine for inhibition of bacterial growth at the site of application. A clear (no bacterial growth) or less dense area will be observed at the site of peptide application in the event of a carry-over. Select the concentration of the inhibitor that results in complete inhibition of the carry-over. 6. Ensure that the inhibitor itself has no effect on bacterial growth. A less dense or a completely clear area observed at the site of inhibitor application would suggest a negative effect on bacterial growth. The use of such inhibitors should be rejected.

3.6. Study Design and Experimental Strategy

1. Use 5–6 skin pieces per group in exploratory studies (e.g., dose range-finding experiments) and 10–12 pieces per group in confirmatory studies that are powered for statistical significance. 2. Ensure that the effect of the vehicle alone on bacterial growth is evaluated, as some formulation excipients may also exhibit antimicrobial activity.

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3. An example of a study design that evaluated the dose– response of an antimicrobial peptide is shown in Table 22.1. Omiganan (formerly MBI 594AN or MBI 226), an antimicrobial peptide currently in clinical development, was used in this study. Skin obtained from antibiotic-free pigs was prepared as described above, inoculated with P. acnes at 2.5 × 106 CFU/skin, and treated 2 h later with 50 ␮L of 0.1– 5% omiganan solutions or vehicle alone (hydro-alcoholic formulation). The control group remained untreated. Following a 24-h incubation at 35±2◦ C in a humidified, anaerobic chamber, the bacterial counts were determined using the swabbing solution supplemented with the peptide inhibitor (1% PSA). Our preliminary experiments indicated that this concentration was sufficient to inhibit all residual peptide activity without causing any negative effect on bacterial growth. This model design resulted in characterization of the dose–response activity of omiganan and also showed that the formulation alone has a small inhibitory effect on bacterial counts (due to the presence of ethanol). The potent antimicrobial activity that omiganan demonstrated in this P. acnes infection model correlated well with the therapeutic activity of omiganan observed in the phase II clinical trial against acne vulgaris (6). 4. An example of the time–response study design is shown in Table 22.2. In this experiment the cationic peptide omiganan was prepared in a 1% gel formulation and applied (100 ␮L/site) to pig skin pieces infected with S. epidermidis (50 ␮L of 2 × 106 CFU/mL). Preliminary

Table 22.1 Dose–response activity of antimicrobial peptide omiganan against P. acnes in pig skin infection model

Treatment

Mean log10 CFU/skin ± SD at 24 h Log10 CFU/skin reduction vs. control posttreatment

No treatment (control)

6.26 ± 0.06∗

Vehicle solution

5.16 ± 0.37

0.1% omiganan solution

4.12 ± 0.18∗

–2.14


4.06 ± 0.07

∗

–2.20


3.19 ± 0.56∗

–3.07


3.35 ± 0.58

∗

–2.91


2.51 ± 0.34

∗

–3.75


2.40 ± 0.77∗

–3.86

∗

p < 0.001 vs. vehicle solution.

–1.10


367

Table 22.2 Time–response activity of antimicrobial peptide omiganan against S. epidermidis in pig skin infection model Log10 CFU/site mean ± SD Treatment

Inoculum (log10 CFU/site) 0 h

1h

Vehicle gel

4.44

4.37±0.57

Omiganan 1.0% gel ∗p

1.64±0.69

4h ∗

8h

4.50±0.37 1.71±0.66

24 h

5.21±0.09 ∗

1.56±0.77

8.33±0.27 ∗

3.14±1.24∗

< 0.001 vs. vehicle gel.

experiments showed that the vehicle gel had no effect on bacterial growth (data not shown). Pig skin pieces were swabbed at 1, 4, 8, and 24 h posttreatment into saline solution containing 1% PSA. This model design allowed for the demonstration that the antibacterial effect of 1% omiganan was very rapid, with significant killing observed at 1 h posttreatment (2.7 log10 CFU/site reduction). At 24 h, a 5.2 log10 reduction was observed as compared to the control sites treated with vehicle alone. When 1% omiganan gel was evaluated in human volunteers, a ≥3 log10 reduction in skin microbial colonization was observed at different time points (7), again indicating a good correlation of the model results with clinical outcomes.

4. Notes 1. Pig skin can be obtained from laboratory pigs or from slaughter houses. The animals should be free from any antibiotic treatment and should not have consumed any antibiotic-supplemented diet for at least 7 days prior to skin sampling. Our preliminary experiments demonstrated that the presence of residual antibiotics in pig skin may result in partial or significant inhibition of bacterial growth. If antibiotic-free animals are impossible to obtain or if information on antibiotic consumption is not available, then the skin should be pretested for its ability to support bacterial growth. 2. Ensure that the plate surface does not have excessive condensation. If the agar surface is even slightly wet, the streaked bacteria may float away and the colonies may not

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be well separated. The plates can be dried by leaving the lids off in a laminar flow hood. 3. Sheep blood agar plates support the growth of all microorganisms and should be used for initial bacterial culture (from stock) to ensure the absence of contamination with other organisms. When growing organisms swabbed from the skin pieces, use specific agar plates (such as TSA, McConkey, or Wilkins–Chalgren agar) that preferably support the growth of the selected organism and thus reducing the possibility of contamination (and sources of error) if the skin was not thoroughly sterilized. 4. Use of disinfectants other than alcohol (for example, iodine, chlorhexidine) is not recommended as they may leave residual amounts on the skin surface, resulting in the inhibition of bacterial growth. 5. If skin collected from several pigs is to be used in one study, skin pieces derived from different animals must be evenly distributed between groups to remove any potential bias related to differences in the skin sources. 6. In addition to the McFarland standard, a spectrophotometer can be used for the adjustment of the bacterial culture in accordance with the manufacturer’s instructions (for example, Spectronic spectrophotometer, model 20D+, Milton Roy). 7. Depending on the goals of the experiment, the final inoculum may vary from 103 CFU/mL (mild infection) to 107 CFU/mL (severe infection). Many organisms will grow rapidly resulting in significant skin infection at 24 h postinoculation, regardless of the initial inoculum size. The exceptions are some very slow growing organisms (e.g., P. acnes) that will show no increase or only a small increase over a 24 h period. An example of typical bacterial growth following infection with low and high inocula is shown in Table 22.3.

Table 22.3 Bacterial growth following skin infection with low and high inocula of S. aureus ATCC 19636 Recovered at 24 h (log10 CFU/site) Applied at time 0 (log10 CFU/site)

n

Mean ± SD

Range

2.70

12

7.83±0.37

7.10–8.47

6.70

12

8.24±0.32

7.77–8.89


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8. For screening purposes, cationic peptides can be formulated in a simple vehicle that is known to have no effect on bacterial growth (e.g., sterile saline). If more complex formulations (such as gels, creams, or ointments) are used, their effect on bacterial growth should be evaluated. See an example of the effect of the ethanol-containing vehicle on bacterial counts (Table 22.1). 9. Smaller volumes (25–50 ␮L) are applied if liquid formulations are used. Larger volumes (100 ␮L) are used when more viscous formulations are employed (gels, creams, or ointments). The general rule is to select a volume that can be evenly spread over the whole skin area as one thin layer. Excessive treatment volumes that result in dripping outside or pooling on the skin must be avoided. 10. A spiral plater (Spiral Biotech) can be used instead of manual plating resulting in significant savings with respect to time and supplies (plates, tubes). References 1. Ray, T.L. (1985) Animal models of experimental Candida infection of the skin. In Models in Dermatology. Maibach, H.I., Lowe, N.J. (Eds.), Vol. 1, pp. 41–50. Basel: S. Karger AG. 2. Jordan, W.E. (1970) The experimental induction of superficial cutaneous infections in guinea pigs J. Invest. Derm. 55, 149–152. 3. Sedlock, D.M. (1985) Animal skin degerming models. In Models in Dermatology. Maibach, H.I., Lowe, N.J. (Eds.), Vol. 2, pp. 131–144. Basel: S. Karger AG. 4. Meyer, W., Schwarz, R., and Neurand, K. (1978) The skin of domestic mammals as a model for the human skin, with special refer-

ence to the domestic pig Curr. Probl. Dermatol. 7, 39–52. 5. Boon, R. J., Beale, A. S., and Sutherland R. (1985) Efficacy of topical mupirocin against an experimental Staphylococcus aureus surgical wound infection. J. Antimicrob. Chemother. 16, 519–526. 6. Friedland, H.D., Sharp, D.D., and Robinson, J.R. (2003) Double-blind, randomized, vehicle-controlled study to assess the safety and efficacy of MBI 594AN in the treatment of acne vulgaris. Abstr. 61st Ann. Meeting Am. Acad. Derm. 61, 22. 7. Isaacson R. E. (2003) MBI-226 Micrologix/Fujisawa Curr. Opin. Invest. Drugs 4, 999–1003.

Chapter 23 Measuring Antimicrobial Peptide Activity on Epithelial Surfaces in Cell Culture Gill Diamond, Sunghan Yim, Isaura Rigo, and Laura McMahon Abstract To more accurately assess the activity and role of epithelial cell-derived antimicrobial peptides in their native settings, it is essential to perform assays at the surfaces under relevant conditions. In order to carry this out, we utilize three-dimensional cultures of airway and gingival epithelium, which are grown at an air–liquid interface. Under these conditions, the cultures can be subjected to challenge with a variety of factors known to cause an increase in antimicrobial peptide gene expression. The functional relevance of this induction can then be assessed by quantifying antibacterial activity either directly on the surface of the cells or using the fluid secreted onto the apical surface of the cultures. The relative contribution of the peptides can also be measured by pre-incubation of the secreted fluid with specific inhibitory antibodies. Thus, a relatively inexpensive in vitro model can be used to evaluate the role of antimicrobial peptides in mucosal epithelium. Key words: Airway, oral epithelium, vitamin D, cathelicidin.

1. Introduction In general, most antimicrobial peptides have been identified by protein purification methods from tissues, followed by in vitro assays to identify the active fraction (see (1–3), for example). Alternatively, DNA sequences coding for homologous peptides are identified through computational or experimental methods (e.g., (4, 5 )). Subsequently, the purified natural peptides or synthetic peptides based on the DNA sequences are characterized by in vitro antimicrobial assays against target organisms, which provide important information regarding the potential for the A. Giuliani, A.C. Rinaldi (eds.), Antimicrobial Peptides, Methods in Molecular Biology 618, DOI 10.1007/978-1-60761-594-1 23, © Springer Science+Business Media, LLC 2010

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peptide’s use as a therapeutic or give clues to its role in innate defense. Furthermore, the expression of many host defense peptide genes is induced by a variety of factors both in cell culture (e.g., (6, 7)) and in vivo (8, 9), supporting their role in innate host defense of mucosal epithelia such as the airway, the oral cavity, and the intestinal tract. However, to accurately assess the relationship between the induction of a peptide gene (as measured by mRNA levels) and an increase in antibacterial activity in a tissue is difficult. Recently, novel methods for cell culture which provide threedimensional model systems that recapitulate the mucosal epithelium for different tissues have been described (10, 11). The systems rely on culturing epithelial cells in an air–liquid interface (ALI) in serum-free medium, leading to well-differentiated cultures, often covered with a cell-derived secretion. This provides an environment that allows for quantification of antimicrobial activity in mucosal secretions under conditions that are more representative of the original tissue and allows the investigator to modulate antimicrobial peptide gene expression with exogenous factors. Assay conditions can then be developed to determine the role of endogenous antimicrobial peptides on mucosal surfaces.

2. Materials 2.1. Airway Epithelial Cell Culture

1. Bronchial epithelial growth media basal medium without growth factors, cytokines, or supplements (BEBM) (Lonza, Walkersville, MD). 2. Bronchial epithelial growth media (BEGM) SingleQuots Kit supplement and growth factors added directly to medium. For 500 mL medium, add bovine pituitary extract (BPE) 2 mL, insulin 0.5 mL, hydrocortisol 0.5 mL, gentamicin sulfate and amphotericin-B 0.5 mL, retinoic acid 0.5 mL, transferrin 0.5 mL, triiodothyronine 0.5 mL, epinephrine 0.5 mL, and hEGF 0.5 mL (Lonza, Walkersville, MD). Antibiotics may be added, but must be removed prior to antimicrobial assays (see Note 1). 3. Costar Transwell permeable supports 12-mm insert, 12-well plate. 4. Collagen from human placenta, type VI. A total of 10 mg is dissolved in 20 mL of dH2 O and 40 ␮L of concentrated acetic acid is added. The collagen is then incubated at 37◦ C for 15–30 min for the collagen to fully dissolve. The stock solution is diluted 1:10 with dH2 O to coat the Transwell inserts.

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5. Normal human bronchial epithelial (NHBE) (Lonza, Walkersville, MD). Other primary cultures may be used (adapted from 11). 2.2. Gingival Epithelial Cell Culture

1. Dulbecco’s Modified Eagle’s Medium with glucose and L -glutamine, supplemented with 10% bovine serum and penicillin–streptomycin. 2. Collagen, type I (rat tail) at 1.1 mg/mL in water with 43 ␮L concentrated acetic acid (33%) per 5 mL of solution is incubated at 37◦ C for 30 min to dissolve the collagen. 3. 10X DMEM (without sodium bicarbonate) powder is prepared in water at 13.48%, filter sterilized, and aliquots are stored at –20◦ C. 4. 10X reconstitution buffer: 22 mg/mL sodium bicarbonate, 20 mM HEPES, 0.62 N NaOH. Aliquots are stored at –20◦ C. 5. Keratinocyte serum-free medium (KSFM) supplemented with L-glutamine. Calcium chloride is added to 0.03 M. Bovine pituitary extract and epithelial growth factor are supplied with the medium and are added as per the manufacturer’s instructions. 6. Costar Transwell permeable supports: 24-mm insert, polyester membrane, 6-well polystyrene plate. 7. OKF6/TERT oral keratinocyte cells are obtained with material transfer agreement from the laboratory of Dr. James Rhinewald, Harvard University (adapted from 12).

2.3. Antimicrobial Assays

1. 10X phosphate-buffered saline solution. 2. 1,25-Dihydroxyvitamin D3 10 ␮g is made to 10–5 M concentration by dissolving it in 100% ethanol. Vitamin D is added to the BEGM medium to make a final concentration of 10–8 M to induce the expression of LL-37. Ethanol is used as a control. 3. LB broth Miller used to grow Pseudomonas aeruginosa in liquid culture and agar plates. 4. Bordet–Gengou agar used to grow Bordetella bronchiseptica on agar plates. 5. Stainer–Scholte medium, used to grow B. bronchiseptica in liquid culture. 6. AAGM (30 g/L of trypticase soy broth or 40 g/L of trypticase soy agar, 6 g/L yeast plus 0.75% dextrose [filter sterilized], and 0.4% sodium bicarbonate [filter sterilized] added after autoclaving) used to grow Aggregatibacter actinomycetemcomitans in liquid culture and agar plates.

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3. Methods Beta-defensins and cathelicidins are antimicrobial peptides expressed in mucosal epithelial cells (reviewed in (13, 14)). Their expression is induced in response to a variety of agents including bacterial lipopolysaccharide (LPS), interleukin (IL)-1␤, and the active form of vitamin D, 1,25(OH)2 D3 (reviewed in (15, 16)). To assess the activity of these peptides in airway epithelial cells, primary cultures of bronchial epithelial cells are grown in an air–liquid interface and are allowed to mature and differentiate for 20 days before any experiments are performed. The bronchial epithelial cells are then basolaterally treated with an inducing agent, such as IL-1␤ (100 ng/mL) or vitamin D at a concentration of 10–8 M. The airway surface fluid (ASF) is then collected by washing the cells with 50 ␮L of filter-sterilized 1X PBS. As a control for the poorly water soluble 1,25(OH)2 D3 , control cells are treated with an equal volume of ethanol. The effect of the inducing agents on the bactericidal activity of ASF is studied using airway pathogens such as B. bronchiseptica or P. aeruginosa. To determine whether specific peptides are responsible for all or part of the activity, the ASF can be pretreated with inhibitory antibodies prior to incubation with bacteria. A relative increase in the number of colonies relative to control (pretreated with nonspecific IgG) suggests a role for that peptide in killing. To quantify the activity of peptides on the surface of gingival epithelial cells, a three-dimensional culture system is used whereby epithelial cells are cultured on Transwells coated with a feeder layer of cells in collagen (10). Once the top layer is confluent, surface medium is removed and the epithelial cells are cultured similar to airway cells in an air–liquid interface. Activity against bacteria is measured using challenge with the periodontal pathogen A. actinomycetemcomitans. 3.1. Airway Epithelial Cell Culture

1. Normal human bronchial epithelial (NHBE) cells are initially grown in monolayer culture by standard tissue culture techniques in BEGM until they reach confluence. 2. To prepare the air–liquid interface system, 12-mm Transwell inserts (see Note 2) are coated with 200 ␮L of diluted type VI collagen. Coated inserts are dried in a laminar flow hood overnight. After the collagen dries the plates are exposed to 30 min of UV light in the hood. 3. Confluent cultures of NHBE cells are washed with 1X HBSS and trypsinized. The trypsin is neutralized with 10% serumbased medium. The cells are then centrifuged at low speed for 5 min and resuspended in BEGM. Cell suspensions are


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counted and seeded in the 12-mm Transwell plates with approximately 250,000 cells per well. Once the cells reach confluence in the 12-mm Transwell inserts the medium is removed from the apical surface of the cells. Cells are kept in a 37◦ C, humidified 5% CO2 incubator. The cells in the Transwell inserts are allowed 20 days to fully mature and differentiate before any experiments are done. The medium in the basolateral chamber is changed every 2–3 days. The apical surface is washed with either PBS or 10 mM phosphate buffer when the medium is changed. 4. Two days before the experiment is carried out, the apical surface is washed twice with 1X PBS and the basolateral medium is replaced with antibiotic-free BEGM. 5. The cells are treated basolaterally with an inducing agent such as 1,25(OH)2 D3 at a final concentration of 10–8 M or with IL-1␤ at 100 ng/mL for up to 48 h. The ASF is collected in 1.5 mL tubes after induction by washing the apical surface of the cells with 50 ␮L of filter-sterilized 1X PBS. ASF is stored in –80◦ C. 3.2. Airway Surface Fluid Antimicrobial Assay

1. P. aeruginosa is streaked from a frozen stock to a LB plate and grown in a 37◦ C incubator overnight. B. bronchiseptica is streaked from a frozen stock to a Bordet–Gengou (BG) agar plate grown in a 37◦ C incubator overnight. 2. A single colony of bacteria is inoculated and grown in liquid culture in a 37◦ C shaking incubator overnight. Bacteria from the overnight liquid culture is diluted 1:10 in fresh medium in a new tube and incubated for 3–6 h in a 37◦ C shaking incubator to obtain bacteria in the mid-log phase of bacterial growth. These bacteria are then diluted to 5 × 104 CFU/mL in 10 mM phosphate buffer. 3. 500 CFU of bacteria (10 ␮L) are mixed with 90 ␮L of the ASF in a 1.5 mL tube. The mixture is incubated in a 37◦ C water bath while shaking at 75 rpm. The contents of the tube are seeded on LB plates (for P. aeruginosa) or BG agar (for B. bronchiseptica) overnight. 4. Bacterial colonies are counted to determine activity of the ASF against the bacteria. An example of the results is shown in Fig. 23.1.

3.3. Inhibition of Activity by Specific Antibodies

1. Bacteria are prepared as above. 2. ASF (90 ␮L) is incubated with 1 ␮L anti-LL-37 or control serum for 1 h at 37◦ C. 3. Bacteria (in 10 ␮L) are added to the ASF mixture and incubated as above. An example of the results is shown in Fig. 23.2.

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Fig. 23.1. Induction of antibiotic activity of airway surface fluid by 1,25(OH)2 D3 . NHBE cells were grown on Transwell CM inserts and exposed to 10–8 M 1,25(OH)2 D3 basolaterally for 0, 24, and 48 h. Antimicrobial activity of ASL against B. bronchiseptica and P. aeruginosa was determined by counting the number of colonies on 5% BG plates supplemented with 5% sheep blood and LB plates, respectively, after incubation with the ASL was collected from the NHBE (Reproduced from (7) with permission from Elsevier Science.).

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Fig. 23.2. Inhibition of antimicrobial activity with LL-37 antibody. ASF was pretreated with 1 ␮L anti-LL-37 antibody (gift of R. Gallo, UCSD) or control serum for 1 h prior to addition of P. aeruginosa in antimicrobial assays as described above. Results are reported as means ± SEM (∗ p < 0.05) of at least three independent experiments. (Reproduced from (7) with permission from Elsevier Science.).


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1. The bronchial epithelial cells in airway–liquid interface are stimulated basolaterally for 24 h. 2. P. aeruginosa is grown in liquid culture overnight (see Note 3) and then diluted 1:10 in new LB broth and incubated for 3–6 h to obtain bacteria in mid-log phase. 3. The mid-log phase bacteria are diluted to 500 CFU in 0.5 ␮L and deposited on the apical surface of the bronchial epithelial cells. After 5 h the apical surface of the cells is washed with 100 ␮L of PBS three times and plated to determine the number of viable colonies.

3.5. Gingival Epithelial Cell Culture

1. Murine fibroblast cells NIH3T3 are grown as a monolayer in a 75 cm2 tissue culture flask at 37◦ C, 5% CO2 in DMEM/bovine serum to 90% confluence using standard tissue culture methods. Normal human gingival cells (OKF6/TERT) are grown as a monolayer in 25 cm2 tissue culture flasks in KSFM to confluence at 37◦ C, 5% CO2 using standard tissue culture techniques. 2. To prepare the air–liquid interface, 24-mm Transwell inserts in a 6-well plate are first coated with 0.8 mL/Transwell of an acellular collagen mixture (see Note 4). For 6 mL (one plate) combine in the following order: 0.6 mL 10X DMEM, 0.6 mL 10X reconstitution buffer, 0.54 mL FBS, 60 ␮L 200 mM L-glutamine, and 4.2 mL collagen solution (to 0.77 mg/mL). Mix by gently swirling and inverting the tube. Try to avoid bubbles. Add 0.8 mL to each Transwell insert. Allow the collagen to solidify at room temperature for 30–60 min. 3. The cellular collagen mixture is then added to the Transwells. For each Transwell, 2.3 mL of the cellular (fibroblast) collagen mixture, containing 5–7 × 105 cells, is required. For one plate combine in the following order: 1.40 mL 10X DMEM 1.40 mL 10X reconstitution buffer 1.56 mL FBS 140 ␮L L-glutamine (200 mM) 9.5 mL collagen solution (for a final concentration of 0.70 mg/mL) (a) Add 1.0 mL of 3T3 cells at 3–4 × 106 /mL, for a final volume of 15 mL. The 3T3 cells are harvested using trypsin EDTA and standard tissue culture methods. After centrifugation, cells are re-suspended in 1 mL DMEM/bovine serum, counted and diluted to 3–4 × 106 /mL with medium. Mix the cellular collagen solution gently by inverting the tube.

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(b) Add 2.3 mL per Transwell on top of the acellular collagen layer and leave in the hood for 45–60 min without moving the plate. Then transfer to 37◦ C, 5% CO2 for 45–60 min, until the collagen gel solidifies. (c) Add DMEM/bovine serum medium: 1.5 mL each inside and outside of the Transwell insert. Continue incubation at 37◦ C, 5% CO2 . 4. At 2–3 days slide a sterile spatula around the edge of the gels, to move them away from the sides of the Transwell inserts. After 5–7 days, the collagen gels should be completely contracted away from the sides of the inserts. Change the medium every 2–3 days. 5. Once the collagen gels have contracted, the epithelial (OKF6/TERT) cells are seeded on the top of the cellular (fibroblast) collagen gels. (a) OKF6/TERT cells are harvested using trypsin EDTA and standard tissue culture techniques, counted, and resuspended to 15 × 106 cells/mL in KSFM. (b) Remove the medium from inside the inserts. Remove about half the medium from outside the inserts. Leave enough so that the bottom of the insert rests completely on the medium, but not so much that the medium rises into the insert. (c) Add 60 mL of the OKF6/TERT suspension on top of the middle of each collagen gel. Confirm OKF6/TERT cell growth by also seeding the same amount of cells into 1 well of a 12-well plate. (d) Incubate at 37◦ C, 5% CO2 for 2 h to allow the OKF6/TERT cells to attach. Then add 2 mL of KSFM to the inserts and 1.2 mL DMEM/bovine serum to the wells and continue incubation at 37◦ C, 5% CO2 . 6. Replace the medium in the inserts with fresh KSFM on the next day and continue at 37◦ C, 5% CO2 , replacing both media every 2 days. 7. After approximately 3–4 days (when the control well has grown to confluence) the inserts can be moved to the air–liquid interface plate containing differentiation medium (BEGM). (a) Add 1.6 mL per well BEGM with antibiotics to a new 6-well tissue culture plate. (b) Remove the medium from inside the Transwells and move each to the new plate. The bottom of the insert should be completely covered with medium, but the medium should not rise into the insert, allowing the cells to be fed from below and the apical surface of the epithe-


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lium to be exposed to air. Incubate the cells at 37◦ C, 5% CO2 for 15 days. Feed every 2–3 days by removing as much medium as possible and add 0.65 mL per well. 8. Equilibrate the cells in antibiotic-free medium. (a) Add 1.6 mL BEGM without antibiotics to each well of a new 6-well tissue culture plate. (b) Remove any medium from inside the Transwells and move each to the new plate. (c) Incubate the cells at 37◦ C, 5% CO2 for 6 days. Every 2–3 days remove as much medium as possible and add 0.65 mL per well BEGM without antibiotics. 3.6. Direct Activity on Gingival Epithelial Cell Surfaces

1. Grow A. actinomycetemcomitans from frozen culture by streaking on an AAGM plate (see Note 3) and incubating at 37◦ C, 10% CO2 for 3–4 days. 2. Use a single colony to inoculate 30 mL of AAGM broth in a 75 cm2 tissue culture flask. Incubate at 37◦ C, 10% CO2 for 40–48 h. The bacteria will grow as a biofilm on the bottom of the flask. 3. The next day, move the Transwell inserts containing the differentiated OKF6/TERT cells equilibrated in antibioticfree medium to a new 6-well plate containing BEGM without antibiotics plus either 1,25-dihydroxyvitamin D3 at 10–8 M or an equal volume of ethanol. Make at least duplicate wells for each treatment. 4. The following day, prepare a single-cell suspension of A. actinomycetemcomitans. (a) Remove the medium from the flask and wash three times with PBS. (b) Add 1 mL PBS, scrape the bacteria into the liquid, and transfer to a microtube. (c) Vortex on the highest speed for 1 min and then allow to settle for 10 min. (d) Transfer the top 750 ␮L, which is the single-cell suspension, to a new microtube. (e) Make a 1:10 dilution and find its absorbance at 595 nm. (f) An OD = 1 corresponds to 2.9 × 106 cfu/mL. 5. Dilute the single-cell suspension to 1 × 103 cfu/␮L in AAGM broth. 6. At 18 h after 1,25-dihydroxyvitamin D3 treatment of the Transwell insert cells, add 500 cfu (0.5 ␮L) to the center of the apical surface of each. 7. Incubate at 37◦ C, 10% CO2 for 1–3 h.

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8. Move each Transwell insert to an unused well. Wash the apical epithelial surface with 50 ␮L of PBS. 9. Remove the PBS wash and plate it on an AAGM agar plate. Repeat for each Transwell insert. 10. Incubate the plates at 37◦ C, 10% CO2 for 3–4 days. 11. Count the colonies present on each plate.

4. Notes 1. Do not forget to change to antibiotic-free medium at least 2 days prior to the assay. 2. Some airway epithelial cells (such as NHBE) can be grown and differentiated in ALI on larger (e.g., 24 mm) inserts, while others require the smaller, 12-mm filters. More ASF can be obtained from the larger filters, so it is best to first determine which size is optimal. The number of cells seeded on the larger filters is increased accordingly. 3. It helps to use bacteria that are resistant to at least one antibiotic. They can be streaked on antibiotic-containing plates, grown in medium with antibiotic, but the antibiotics should be washed out during processing prior to assays. Final plating on antibiotic-containing plates will then only identify the bacteria that were intentionally added to the assay. 4. For the gingival epithelial cell Transwell preparation: (a) Bovine collagen type I can also be used. If bought as a prepared solution (Organogenesis is one source), it is usually stored at 4◦ C. Test to see if it solidifies at room temperature. If it does, use pre-chilled pipettes and keep the solutions on ice. Do a trial run to see if this will cause the fibroblasts to lyse. If the collagen solution does not solidify at room temperature, warm at 37◦ C for 15 min before use and keep all reagents at room temperature during preparation of the collagen layers. (b) Adjust the amount of FBS in both the acellular and cellular collagen mixtures to maintain final collagen concentrations of 0.77 and 0.70 mg/mL, respectively. (c) Observe the collagen as it is mixed into each solution to see that it mixes in completely. (d) A confluent 75 cm2 tissue culture flask of 3T3 cells (fibroblasts) contains more than enough cells for two Transwell plates.


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(e) After 2–3 days, free up the edges of the collagen gels using either a sterile pipette tip or a sterile metal spatula. (f) For the epithelial layer (TERT cells), two to three confluent 25 cm2 flasks are needed for one Transwell plate.

Acknowledgments The authors would like to thank Drs. Leslie Fulcher and Scott Randell (University of North Carolina, Chapel Hill) and Helena Kashleva and Anna Dongari-Bagtzoglou (University of Connecticut) for assistance in growing the ALI cultures of airway and gingival cells, respectively. GD is supported by grants from the Cystic Fibrosis Foundation and the NIH (DE18781). References 1. Cole, A. M., Weis, P., and Diamond, G. (1997) Isolation and characterization of pleurocidin, an antimicrobial peptide in the skin secretions of winter flounder. J. Biol. Chem. 272, 12008–12013. 2. Diamond, G., Zasloff, M., Eck, H., Brasseur, M., Maloy, W. L., and Bevins, C. L. (1991) Tracheal antimicrobial peptide, a novel cysteine-rich peptide from mammalian tracheal mucosa: peptide isolation and cloning of a cDNA. Proc. Natl. Acad. Sci. USA 88, 3952–3956. 3. Harder, J., Bartels, J., Christophers, E., and Schroder, J. -M. (1997) A peptide antibiotic from human skin. Nature 387, 861. 4. Bals, R., Goldman, M. J., and Wilson, J. M. (1998) Mouse ␤-defensin 1 is a salt-sensitive antimicrobial peptide present in epithelia of the lung and urogenital tract. Infect. Immun. 66, 1225–1232. 5. Garcia, J. R., Krause, A., Schulz, S., Rodrigues-Jimenez, F. J., Kluver, E., Adermann, K., Forssmann, U., FrimpongBoateng, A., Bals, R., and Forssmann, W. G. (2001) Human beta-defensin 4: a novel inducible peptide with a salt-sensitive spectrum of antimicrobial activity. FASEB J. 15, 1819–1821. 6. Diamond, G., Russell, J. P., and Bevins, C. L. (1996) Inducible expression of an antibiotic peptide gene in lipopolysaccharidechallenged tracheal epithelial cells. Proc. Natl. Acad. Sci. USA 93, 5156–5160. 7. Yim, S., Dhawan, P., Ragunath, C., Christakos, S., and Diamond, G. (2007) Induc-

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tion Of Cathelicidin In Normal And CF Bronchial Epithelial Cells By 1,25Dihydroxyvitamin D3. J. Cystic Fibrosis 6, 403–410. Caverly, J. M., Diamond, G., Gallup, J. M., Brogden, K. A., Dixon, R. A., and Ackermann, M. R. (2003) Coordinated expression of tracheal antimicrobial peptide and inflammatory-response elements in the lungs of neonatal calves with acute bacterial pneumonia. Infect. Immun. 71, 2950–2955. Stolzenberg, E. D., Anderson, G. M., Ackermann, M. R., Whitlock, R. H., and Zasloff, M. (1997) Epithelial antibiotic induced in states of disease. Proc. Natl. Acad. Sci. USA 94, 8686–8690. Dongari-Bagtzoglou, A. and Kashleva, H. (2006) Development of a highly reproducible three-dimensional organotypic model of the oral mucosa. Nat. Prot. 1, 2012–2018. Fulcher, M. L., Gabriel, S., Burns, K. A., Yankaskas, J. R., and Randell, S. H. (2005) Well-differentiated human airway epithelial cell cultures. Methods Mol. Med. 107, 183–206. Dongari-Bagtzoglou, A. and Kashleva, H. (2006) Development of a novel three-dimensional in vitro model of oral Candida infection. Microb. Pathog. 40, 271–278. Brogden, K. A. (2005) Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria?. Nat. Rev. Microbiol. 3, 238–250.

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14. Hancock, R. E. W. and Diamond, G. (2000) The role of cationic antimicrobial peptides in innate host defences. Trends Microbiol. 8, 402–410. 15. Diamond, G., Beckloff, N., and Ryan, L. K. (2008) Host defense peptides in the oral cavity and the lung: similarities and differences. J. Dent. Res. 87, 915–927.

16. Diamond, G., Laube, D., and KleinPatel, M. E. (2004) In Mammalian Host Defence Peptides. R. E. W. Hancock and D. A. Devine (Eds.), Vol. 6, pp. 111– 138. Cambridge, UK: Cambridge University Press.

Chapter 24 Antimicrobial and Antibiofilm Activity of Quorum Sensing Peptides and Peptide Analogues Against Oral Biofilm Bacteria Karen LoVetri and Srinivasa Madhyastha Abstract Widespread antibiotic resistance is a major incentive for the investigation of novel ways to treat or prevent infections. Much effort has been put into the discovery of peptides in nature accompanied by manipulation of natural peptides to improve activity and decrease toxicity. The ever increasing knowledge about bacteria and the discovery of quorum sensing have presented itself as another mechanism to disrupt the infection process. We have shown that the natural quorum sensing (QS) peptide, competence-stimulating peptide (CSP), used by the caries causing bacteria Streptococcus mutans when used in higher than normally present concentrations can actually contribute to cell death in S. mutans. Using an analogue of this quorum sensing peptide (KBI-3221), we have shown it to be beneficial at decreasing biofilm of various Streptococcus species. This chapter looks at a number of assay methods to test the inhibitory effects of quorum sensing peptides and their analogues on the growth and biofilm formation of oral bacteria. Key words: Streptococci, quorum sensing (QS) peptides, competence stimulating peptide (CSP), analogue, antibiofilm.

1. Introduction Bacteria use a cell-to-cell communication system called “quorum sensing” (QS) to obtain information on bacterial density in their environment for regulating the expression of genes involved in virulence and biofilm formation in response to fluctuations in cell density (1). Gram-positive bacteria such as Streptococci use short peptides called “competence stimulating peptide” (CSP), a quorum sensing (QS) molecule, which requires a two-component (histidine kinase receptor and response regulator) transduction system for detection and function (2). Although Streptococci A. Giuliani, A.C. Rinaldi (eds.), Antimicrobial Peptides, Methods in Molecular Biology 618, DOI 10.1007/978-1-60761-594-1 24, © Springer Science+Business Media, LLC 2010

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constitute 60–90% of the early colonizers of dental plaque, Streptococcus mutans is the principal etiological agent of dental cavities (3). As the quorum sensing in S. mutans is known to regulate a number of physiological activities including biofilm development (2), inhibition of the quorum sensing pathway would be the best approach for attenuating S. mutans virulence. We have designed and synthesized a peptide analogue (KBI-3221) based on the S. mutans CSP molecule to specifically target the quorum sensing system and inhibit the process of biofilm development (4). The procedures outlined in this chapter include 96-well and 12-well microtiter plate assays to determine the inhibitory effects of quorum sensing peptide and its analogue on planktonic growth as well as biofilm formation of oral bacteria and also on biofilmembedded oral bacteria. In addition, the hydroxyapatite disk assay is used to mimic the tooth surface as an adhesive surface for the typical oral bacteria, and colony counts are used to assess the effectiveness of the peptide and/or analogue in question. Furthermore, confocal scanning laser microscopy is used to visualize the effect of the CSP peptide on biofilm formation in S. mutans.

2. Materials 2.1. Cell Culture and Peptide Synthesis

1. Glycerol (15%) stock of oral bacteria. Stored –80◦ C. Streptococcal strains used: S. mutans (UA159), S. oralis (NCTC11472), and S. sobrinus (HNG909S). 2. Todd Hewitt Yeast Extract (THYE) Agar: Todd Hewitt Broth (Oxoid, Nepean, ON, Canada), 3% yeast extract, and 15% agar. 3. Sterile 100 × 15 mm petri plates. 4. Todd Hewitt Yeast Extract Broth + mucin: Todd Hewitt Broth, 3% yeast extract, 0.01% hog gastric mucin, pH 7.0. 5. Sterile 12 mL culture tubes (Simport, Thermo Fisher Scientific, Nepean, ON, Canada). 6. Anaerobic incubation conditions: GENbag Anaer bags and sachets (bioMerieux, Montreal, Canada) and/or BD GasPak EZ Anaerobe (Thermo Fisher Scientific, Nepean, ON, Canada). 7. Spectrophotometer Genesys 10uv (Thermo Fisher Scientific Nepean, ON, Canada). 8. CSP (SGSLSTFFRLFNRSFTQALGK) and its analogue (see Note 1), KBI-3221 (SGSLSTFFRLFNASFTQALGK) are synthesized by Mimotopes (Roseville, MN, USA) using the

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following parameters. The qualitative analysis of the peptides is done by electrospray mass spectrometry (ESMS) and purified to 90% by reverse phase-high performance liquid chromatography (RP-HPLC) on a 150 × 4.6 mm Monitor C18 column with a gradient of acetonitrile (10–66.6%) in 0.1% trifluoroacetic acid for 25 min. The peptides are readily solubilized in sterile double-distilled reverse osmosis water and stored in aliquots at –20◦ C.

2.2. 96-Well Biofilm Assay

1. Semi-defined minimal (SDM) medium is prepared in five parts as shown in Table 24.1. All stock solutions are prepared in sterile double-distilled reverse osmosis water unless otherwise indicated. To prepare SDM medium with supplements, add 2.0 mL of Casamino acids, 1.0 mL of glucose, 1.0 mL of amino acid mixture, 1.0 mL of vitamins to every 10 mL of SDM (see Note 2). Adjust the pH of the mixture to 7.0 with 1.0 N HCl, followed by filter sterilization. 2. 96-well (flat bottom) polystyrene microtiter plates (costar 3598, Corning Inc., Corning, NY).

Table 24.1 Composition of the semi-defined minimal (SDM) medium and additives

Composition

Stock concentration g/L

SDMa Potassium phosphate dibasic (K2 HPO4 )

Composition

Stock concentration mg/100 mL

Amino acidsb (10× stock) 10.1

L -Glutamic

acid

588.52

Potassium phosphate (KH2 PO4 )

2.0

L -Arginine

HCl

210.66

Ammonium sulfate (NH4 SO4 )

1.3

L -Cysteine

HCl

204.9

Sodium chloride (NaCl)

2.0

L -Tryptophan

Magnesium sulfate (MgSO4 . 7 H2 O)

0.2

0.2% Casamino acidsa Casamino acids

Vitaminsb (10× stock) 10

200 mM Glucosec Dextrose (C6 H12 O6 )

a b c

2.04

27

Mix, autoclave, and store at room temperature (see Note 3). Mix, filter sterilize, and store at 4◦ C (see Note 4). Mix, filter sterilize, and store at room temperature (see Note 4).

Nicotinic acid

4.92

Pyridoxine HCl

20.56

Pantothenic acid

2.38

Riboflavin

0.376

Thiamine HCl

0.1

D -Biotin

0.12

386


3. Microtiter plate reader (Multiskan Ascent, Labsystems, Helsinki, Finland). 4. Stain solution: 0.4% (w/v) crystal violet. Heat on low and stir until it completely dissolves. Let it cool and store at 4o C. 5. Solubilizing solution: 33% (v/v) acetic acid. Store at room temperature. 2.3. 12-Well Biofilm Assay

1. 0.25% THYE broth + 0.01% hog gastric mucin medium and adjust to pH 7.0 using 1 N HCl, autoclave, store at room temperature. 2. 12-well polystyrene microtiter plate (Costar 3513, Corning Inc., Corning, NY). 3. Phosphate-buffered saline (PBS): Prepare 10 × stock with 1.37 M NaCl, 27 mM KCl, 100 mM Na2 HPO4 , 18 mM KH2 PO4 (adjust to pH 7.4 with 1 N HCl if necessary) autoclave, store at room temperature. Dilute 100 mL with 900 mL sterile double-distilled reverse osmosis water for use. 4. Sonicator FS 20 (Fisher Scientific, Nepean, ON, Canada).

2.4. Hydroxyapatite Disk (HAD) Assay

1. HAD (Clarkson Chromatography Products Inc., South Williamsport, PA, 0.38 dia. × 0.06–0.08 thick). 2. Physiological saline: 0.9% (w/v) sodium chloride. Autoclave and store at room temperature. 3. Sterile 12 mL culture tubes. 4. Sonicator FS20. 5. Vortex mixer (Fisher Scientific, Nepean, ON, Canada).

2.5. Confocal Scanning Laser Microscopy (CSLM)

1. Fluorescent stain solution: 2% (w/v) Wheat germ R conjugate (W11261 Invitroagglutinin–Alexa Fluor 488 gen, Burlington, ON, Canada) in PBS (see Note 5). 2. Olympus IX-70 CSLM with an argon laser (Carson Scientific, Markham, ON, Canada). 3. Fluoview software and Image Pro-Plus software (Carson Scientific, Markham, ON, Canada).

3. Methods It is important to have rapid, sensitive, and reliable methods to test the effects of quorum sensing peptides and their analogues on the growth and biofilm formation of oral bacteria. The 96-well assay provides a simple and rapid method for the initial screening of peptides for antimicrobial as well as antibiofilm activity. The results of the 96-well assay can be further confirmed by the


387

12-well assay wherein you count the surviving cells in terms of colony forming units in order to confirm the peptide activity. The HAD assay is particularly relevant to testing a peptide activity against oral bacteria whereby the tooth surface is mimicked by using the hydroxyapatite disk thus allowing for the oral bacteria to behave in a more natural manner in terms of adhesion. Additionally, it is possible to visualize the bacterial biofilm formation on HAD in the presence and absence of peptide with the confocal scanning laser microscopy which is a further proof of biofilm inhibition. 3.1. Bacterial Culture for Assays

1. All Streptococcus spp. cultures are started from glycerol stock by streaking onto THYE agar plates. 2. The plates are incubated at 37◦ C for 48 h under anaerobic conditions in the GENbag system. After using the plate, it can be stored for a further 48 h at 4◦ C (see Note 6). Overnight cultures are prepared by aliquoting 3 mL of THYE & mucin broth into a 12 mL sterile tube, inoculating heavily from the plate into the broth. 3. Static incubation is carried out at 37◦ C for 16–18 h under anaerobic conditions. 4. The optical density of culture is measured at 600 nm and the cultures having an optical density between 1.0 and 1.3 are chosen (see Note 7).


1. The 96-well biofilm assay is based on a previously described method of Cvitkovitch et al. (4). Biofilm is developed in 96well (flat bottom) polystyrene microtiter plates. 2. Growth of static biofilm is initiated by inoculation of overnight culture at 3.3% into the semi-defined minimal (SDM) medium with supplements. Biofilm is grown in the presence of CSP or KBI-3221 and in water for control (20 ␮L of peptide or water in a total volume of 200 ␮L/well). 3. Plates are statically incubated at 37◦ C for 16 h under anaerobic conditions. 4. Growth of planktonic cells is determined by measuring absorbance at 600 nm using a microtiter plate reader. 5. Biofilm is measured by discarding medium with planktonic cells (see Note 8) and rinsing with 200 ␮L of water (once). Air dry the plate overnight (see Note 9). 6. The bound cells are stained for 15 min by adding 200 ␮L of stain solution (see Note 8). 7. Stain solution is removed (see Note 8) and wells are rinsed with 200 ␮L water (three times) and let the plate air dry for 15 min.

388


8. Add 200 ␮L of solubilizing solution and let the plate sit for 15 min and measure absorbance at 630 nm using a microtiter plate reader. 9. For each experiment, background staining is corrected by subtracting the staining solution bound to controls. All comparative analyses are conducted by incubating strains in the same microtiter plate to minimize variability Fig. 24.1. S. mutans

S. so brinus

S. o ralis

Absorbance

1.6 1.2

*

0.8

*

0.4

*

0

Control

KBI-3221 (20 µg/ml)

Control

OD 600

KBI-3221 (20 µg/ml)

Control

KBI-3221 (20 µg/ml)

OD 630

Fig. 24.1. Antibiofilm activity of KBI-3221 against oral streptococci (as determined by the 96-well biofilm assay. Planktonic growth and stained biofilm were measured at 600 and 630 nm, respectively. Values are expressed as mean ± SD. Asterisks (∗ ) indicate a significant difference (P < 0.05) in biofilm inhibition between treated and untreated).


1. A slightly modified 12-well biofilm assay is based on a previously described method of Li et al (2). 2. The static biofilms are developed in a 12-well polystyrene microtiter plate. 3. Growth of biofilm is initiated by inoculation of overnight culture at 1.0% into 0.25 dilute THYE + 0.01% hog gastric mucin medium. 4. Wells contain either CSP or KBI-3221 or water as control (200 ␮L of peptide or water in a total volume of 2 mL/well). 5. Plates are statically incubated at 37o C under anaerobic conditions for 20 h. 6. Planktonic cells are removed (see Note 10) and wells are rinsed once with 2 mL PBS. 7. Biofilm cells are suspended in 2 mL of PBS and then plate is sonicated (see Note 11) for 15 s. 8. The cells are serially diluted (see Note 12) in PBS and plated on THYE agar. Plates are incubated at 37o C under anaerobic conditions and viable cell counts are taken after 48 h (Fig. 24.2).


389

log CFU/ml

6.0 5.0 4.0 3.0 2.0 1.0 0.0 Control (0)

CSP (100)

Concentration (µg /ml) Fig. 24.2. Antibiofilm activity of CSP against biofilm-embedded S. mutans (as determined by the 12-well biofilm assay. Biofilm-embedded bacteria was measured by CFU counts).

1. The HAD assay is based on a previously described method (5). The experiment is carried out using 12 mL sterile culture tubes. 2. Growth of biofilm is initiated by inoculation of overnight culture at 1.0% into 0.25 dilute THYE + mucin medium. 3. The 12 mL tubes contain 4.5 mL inoculum and either 500 ␮L of CSP or KBI-3221 or control (water). 4. The sterile HAD was added to the tubes and was incubated for 24 h at 37◦ C under stationary anaerobic conditions. 5. The disks are washed (three times) in 5 mL physiological saline (see Note 13). 6. Washed disks are added using sterile tweezers to 5 mL fresh physiological saline. 7. The disks are sonicated for 30 s, followed by 1 min of vortexing. 8. Plate appropriate dilutions (see Note 12) onto THYE agar. 9. Plates are incubated at 37◦ C under anaerobic conditions and viable cell counts are taken after 48 h (Fig. 24.3). 7 6

log CFU/ml

3.4. Hydroxyapatite Disk (HAD) Assay

5 4 3 2 1 0 Control (0)

CSP (100)

Concentration (µg/ml) Fig. 24.3. Antibiofilm activity of CSP against biofilm-embedded S. mutans on hydroxyapatite disks (as determined by the hydroxyapatite assay. Biofilm-embedded bacteria were measured by CFU counts).

390


3.5. Confocal Scanning Laser Microscopy (CSLM)

1. The biofilms are grown on HADs as per steps 2–4 from Section 3.4. 2. Disks are washed twice in 5 mL PBS (see Note 13). 3. Disks are removed and transferred to new culture tubes containing 500 ␮L of the fluorescent stain solution. This lectin conjugate binds to N-acetylglucosamine in biofilms of both Gram-positive and Gram-negative bacteria. 4. The disks are incubated for 2 h (in dark) at 4◦ C. 5. The disks are washed twice in 5 mL of PBS (see Note 13). 6. The disks are air dried for 30 min (in dark). 7. Biofilms are observed using an Olympus IX-70 CSLM with an argon laser for excitation at 488 nm (green fluorescence) (6). 8. Images are captured and processed by using Fluoview software and Image Pro-Plus software (Fig. 24.4). A

B

Fig. 24.4. Confocal images of S. mutans growing on hydroxyapatite disks in the absence (a) and the presence of CSP (b) (100 ␮g/mL).

4. Notes 1. The analogue of CSP has only one amino acid change the arginine (R) to alanine which is reflected by the A. 2. To have enough SDM medium with additives for one 96well plate, you will have to double these amounts. 3. After autoclaving, the SDM medium will have some precipitate, shake well before using to evenly distribute.


391

4. Filter sterilization is done through a low protein binding hydrophilic polyethersulfone membrane with 0.20 ␮m pore size into a sterile tube. 5. Before preparing fluorescent stain solution thaw and spin (13,000×g × 30 s) wheat germ agglutinin-Alexa Fluor R 488 to precipitate any particulates. 6. Store streptococci cultures no longer than 48 h at 4◦ C. 7. It is important to optimize the assay with your particular strain of Streptococcus spp. The optical density is measured at 600 nm of multiple overnight cultures to obtain optimal cell density. The following are examples of 600 nm readings when 10 ␮L of overnight culture is added to 990 ␮L THYE + mucin broth: S. mutans = 1.0–1.2 (≤107 –108 CFU/mL), S. oralis = 1.1–1.3 (≤107 –109 CFU/mL), and S. sobrinus = 1.0–1.2 (≤107 –108 CFU/mL) 8. Multi and single channel pipetting is a crucial aspect to all assays described. For the 96-well assay, when initially removing the planktonic cells it is important to gradually allow the pipette to pull up the planktonic medium as you slowly lower the pipette deeper into the wells, trying to keep the pipette tips in the center of each of the wells. When adding the water or stain solution into the wells for the initial wash as well as subsequent washes and the staining, hold the pipette above the wells and slowly allow the 200 ␮L of water or stain solution to go into the well a few drops at a time. 9. When air drying overnight, remove the plate lid and wrap the plate with a kimwipe. 10. Pipetting in the 12-well assay is crucial. It is important to remove the planktonic medium as slowly as possible and position the pipette tip in the same position in the well each time. When washing ensure that you dispense the water slowly near the top of the well to not disturb the biofilm. Remove the wash as slowly as possible and position the pipette tip in the same position in the well. 11. To avoid contamination between wells in the 12-well plate, stretch a layer of parafilm over the top of the wells then press lid on tightly. 12. After the sonication, ensure you remove the appropriate quantity from the well/tube by first pipetting a few times to get a good mix and break up of biofilm cells that you will be adding to the dilution tubes. When diluting give tubes firm shaking to create a good dispersal of the biofilm cells as the oral bacteria tend to clump.

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13. When rinsing the HAD use sterile tweezers which are angled at the top of the tube to stop the disk from falling out of the tube.

References 1. H˚avarstein, L. S. and Morrison, D. A. (1999) Quorum sensing and peptide pheromones in streptococcal competence for genetic transformation. In Cell–Cell Signaling in Bacteria. G. M. Dunny and S. C. Winans (Eds.), pp. 9–192. Washington, DC: ASM Press. 2. Li, Y. H., Lau, P. C. Y., Lee, J. H., Ellen, P., and Cvitkovitch, D. G. (2001) Natural genetic transformation of Streptococcus mutans growing in biofilms. J. Bacteriol 183, 897–908. 3. Emilson, C. -G. and Krasse, B. (1985) Support for and implications of the specific plaque hypothesis. Scand. J. Dent. Res. 93, 94–104. 4. Cvitkovitch, D. G., Lau, P. C. Y., and Li, Y. H. (2001) Signal peptides, nucleic

acid molecules and methods for treatment of caries. Canadian Patent Application 2332733. 5. Sieck, B., Takagi, S., and Chow, L. C. (1990) Assessment of loosely bound fluoride uptake by tooth enamel from topically applied fluoride treatments. J. Dent. Res. 69, 1261–1265. 6. Burton, E., Gawande, P. V., Yakandawala, N., LoVetri, K., Zhanel, G. G., Romeo, T., Friesen, A. D., and Madhyastha, S. (2006) Antibiofilm activity of GlmU enzyme inhibitors against catheter-associated uropathogens. Antimicrob. Agents. Chemother. 50, 1835–1840.

Chapter 25 Characterization of the Leishmanicidal Activity of Antimicrobial Peptides ´ Luque-Ortega and Luis Rivas Juan Roman Abstract This chapter describes the basic methodology to assay the activity of antimicrobial peptides (AMPs) on Leishmania, a human protozoan parasite. The protocols included can be methodologically divided into two major blocks. The first one addresses the basic technology for growth of the different stages of Leishmania, assessment of leishmanicidal activity, and monitoring of plasma membrane permeabilization. The second block encompasses the monitoring of bioenergetic parameters of the parasite, visualization of structural damage by transmission electron microscopy, or those methods more closely related to the involvement of intracellular AMP targets, as subcellular localization of the peptide and induction of parasite apoptosis. Key words: Leishmania, membrane permeabilization, electron microscopy, confocal microscopy, apoptosis, antimicrobial peptide, axenic amastigote.

1. Introduction Protozoa are one of the most neglected targets for antimicrobial peptides (AMPs). Historically, this is due to several reasons: first, the limited knowledge on the biology of these organisms compared to higher eukaryotes; second, the often difficult conditions for their growth, particularly when scale-up is concerned (1); and third, and most important, the relative lack of interest of big pharma in parasitic diseases, mostly confined to countries with low-income populations that are unable to meet the cost even of classical chemotherapy (2), much less those of a peptidebased treatment. Despite these caveats, protozoa constitute a very A. Giuliani, A.C. Rinaldi (eds.), Antimicrobial Peptides, Methods in Molecular Biology 618, DOI 10.1007/978-1-60761-594-1 25, © Springer Science+Business Media, LLC 2010

393

394

Luque-Ortega and Rivas

interesting model of pathogen-innate immunity interplay for several reasons: to ensure dissemination they must establish longterm infections (3), where survival to the host immune response – including components of its innate branch (4) – is mandatory (5); their often complex life cycles may involve intracellular stages (6), as well as substantial changes in membrane architecture (7), all of which entail significant changes in their interaction with AMPs. With few exceptions, such as the cyst stage of parasitic protozoa transmitted by environmental contamination, parasitic protozoa are devoid of compactly packed external barriers such as the outer membrane of Gram-negative bacteria, the thick peptidoglycan layer in Gram-positive, or the fungal wall. In the context of AMP action, this situation favors direct interaction with the plasma membrane, without intervening barriers, and thus allows a relatively straightforward interpretation of the results. The different species of the genus Leishmania are responsible for a group of human infections collectively grouped as leishmaniasis. These encompass a wide variety of clinical symptomatologies, from the self-healing forms, associated to some cutaneous leishmaniasis, to the visceral ones, fatal if untreated. The parasite shows a digenic cycle with two major forms: the promastigote, the flagellated form, and the intracellular amastigote form, which lives inside mononuclear phagocytic cells of a wide variety of mammals (8). Leishmania is in several aspects an atypical target for AMPs: (i) endocytosis and exocytosis processes are restricted to flagellar pocket, a specialized area of the plasma membrane devoid of subpellicular microtubules (9), which somehow limits the repairing capacity of the plasma membrane; (ii) the plasma membrane of the promastigote possesses a thick anionic glycocalix made up mostly of lipophosphoglycan (10) and an abundant external GPIanchored Zn2+ metalloproteinase called Gp63 or leishmanolysin (11), both of which are known to be involved in partial resistance against AMPs (12, 13); (iii) while the amastigote stage would appear more vulnerable than promastigote one due to a much less developed glycocalix, both its location inside the parasitophorous vacuole and likely changes in phospholipid composition of its plasma membrane impose additional hurdles for AMP action. Although from an anti-Leishmania therapeutic perspective, the only data required for a given AMP are its leishmanicidal activity and therapeutic index, our goal in this chapter is to provide the reader with a collection of methods helpful in defining the leishmanicidal mechanisms and establishing a correlation among lethal activity and other effects of the AMPs, such as membrane permeation activity or variation of bioenergetic parameters of the parasite, which can direct further to SAR studies. Furthermore, protocols to assess structural damage to the parasite, based on

Antimicrobial Peptide Assay on Leishmania

395

transmission electron microscopy, or for clues about the involvement of intracellular targets such as subcellular destination of the AMP assessed by confocal microscopy and induction of apoptosis, were also included. In this chapter, AMP activity will be mostly referred to extracellular parasites, these being not only promastigotes but also pertaining to the axenic Leishmania pifanoi amastigote line, whose similarity to the amastigotes isolated from infected macrophages has been exhaustively demonstrated (14–16). We recommend assaying axenic amastigotes, available for a wide variety of Leishmania species (17), before performing the timeconsuming and labor-consuming AMP tests on Leishmaniainfected macrophages, despite the much closer similarity of the latter model to the physiology of infection. In the long run, the development of new imaging systems may overcome some of the aforesaid limitations and make high-throughput analysis of infected macrophages a reality (18–23).

2. Materials 2.1. Cell Culture

1. RPMI 1640 medium, supplemented with 10% heatinactivated fetal calf serum (HIFCS), 25 mM HEPES, 2 mM L -glutamine, 100 units/mL sodium benzyl penicillin, and 48 ␮g/mL gentamicin at pH 7.2 (RPMI 1640 + HIFCS). Sterilize this medium in a vertical laminar flow hood by filtering through a sterile filtration device fitted with a 0.22 ␮m nitrocellulose filter. Store at 4◦ C (see Note 1). 2. M199 medium, supplemented with 20% HIFCS, 2.5% (w/v) trypticase peptone, 13.8 mM D-glucose, 76 ␮M hemin, and 48 ␮g/mL gentamicin sulfate at pH 7.2 (M199 + HIFCS). Sterilize this medium as in Step 1 of Section 2.1. Store at 4◦ C (see Note 2). 3. Hanks balanced salt solution supplemented with D-glucose (HBSS): 137 mM NaCl, 5.3 mM KCl, 0.4 mM KH2 PO4 , 4.2 mM NaHCO3 , 0.4 mM Na2 HPO4 , pH 7.2, 10 mM Dglucose. Adjust to pH 7.2 if necessary. Sterilize as in Step 1 of Section 2.1 (see Note 3).

2.2. Cell Proliferation Measurements

1. Sterile Hanks balanced salt solution (HBSS) described in Step 3 of Section 2.1. 2. RPMI 1640 medium devoid of phenol red, supplemented with 10% HIFCS, 25 mM HEPES, 2 mM L-glutamine, 100 units/mL sodium benzyl penicillin, 48 ␮g/mL gentamicin

396


sulfate, at pH 7.2. Sterilize as in Step 1 of Section 2.1. Store at 4◦ C. 3. M199 + HIFCS medium for amastigotes (described in Step 2 of Section 2.1 ). 4. [3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] (MTT) (Sigma Chemical Co., St. Louis, MO, USA) stock solution: 5 mg/mL in sterile HBSS. Store as single-use aliquots at –20◦ C (this compound is light sensitive). Prepare fresh working solutions at the desired concentration by dilution with HBSS. 5. Sodium dodecyl sulfate (SDS): USP/NF quality, 10% (w/v) aqueous solution. 6. Sterile 96-well microplates. 2.3. Cytotoxicity Against Intracellular Amastigotes

polystyrene

tissue

culture-treated

1. RAW 264.7 murine macrophage cell line (alternatively, mouse peritoneal macrophages can be used) (see Note 4). 2. Lab-Tek 16-well chamber slide system (Nalge Nunc, Rochester, NY, USA). 3. Sterile RPMI 1640 + HIFCS medium, as described in Step 1 of Section 2.1. 4. Sterile RPMI 1640 medium supplemented with 2% HIFCS. 5. Sterile HBSS, as described in Step 3 of Section 2.1. 6. Giemsa’s azur eosin methylene blue solution (Merck, Darmstadt, Germany). 7. Methanol (Merck). R mounting medium (Fluka, Buchs, Switzerland). 8. Eukitt

2.4. Assessment of Plasma Membrane Permeabilization by AMPs

1. SYTOX Green (Invitrogen, Carlsbad, CA, USA): 500 ␮M stock solution in DMSO. Store in small aliquots (20 ␮L) at –20◦ C, shielded from light. Prepare fresh working solution (2 ␮M) in HBSS.

2.4.1. Entrance of Vital Dyes

2. HBSS, as described in Step 3 of Section 2.1. 3. Triton X-100: 1% (w/v) in H2 O. 4. Black polystyrene 96-well microplates (Nunc, Roskilde, Denmark). 5. Fluorescence microplate reader, equipped with excitation and emission filters of 485 and 520 nm, respectively.

2.4.2. Plasma Membrane Depolarization

1. Bisoxonol [bis-(1,3-diethylthiobarbituric) trimethine oxonol] (Invitrogen): 100 ␮M stock solution in DMSO. Store at –20◦ C, shielded from light. Prepare fresh working solution (0.2 ␮M) by dilution in HBSS.


397

2. HBSS, as described in Step 3 of Section 2.1. 3. Gramicidin D (Sigma): 8 ␮M stock solution in HBSS (see Note 5). 4. Black polystyrene 96-well microplates. 5. Fluorescence microplate reader, equipped with excitation and emission filters of 544 and 584 nm, respectively. 2.5. Mitochondrial Membrane Depolarization

1. Rhodamine 123 [2-(6-Amino-3-imino-3H-xanthen-9yl) benzoic acid methyl ester, chloride] (Invitrogen): 0.1 mg/mL stock solution in DMSO. Prepare fresh working solution (0.3 ␮g/mL) in HBSS. 2. HBSS, as described in Step 3 of Section 2.1. 3. KCN: 10 mM stock solution in HBSS, to be made fresh. Beware, this substance is highly toxic. Handling and disposal according to local regulations.

2.6. Oxygen Consumption Rate

2.7. Confocal Microscopy

1. Respiration buffer: 10 mM Tris–HCl, pH 7.2, 125 mM saccharose, 65 mM KCl, 1 mM MgCl2 , 2.5 mM NaH2 PO4 , 0.3 mM EGTA, and 5 mM sodium succinate. Readjust pH to 7.2, if necessary. R 1. Printed microscope slides (Cel-Line , Menzel GmbH, Braunschweig, Germany).

2. HBSS, as described in Step 3 of Section 2.1. 3. Phosphate buffered saline (PBS) stock solution (2X): 274 mM NaCl, 5.4 mM KCl, 16 mM Na2 HPO4 , 3 mM KH2 PO4 . Adjust to pH 7.2 with HCl. 4. MitoTracker Red CMXRos (Invitrogen): 100 ␮M stock solution in DMSO. Store at –20◦ C, shielded from light. Prepare fresh working solution (0.1 ␮M) in HBSS for each assay. hydrochloride) 5. DAPI (4 ,6-diamidino-2-phenylindole (Invitrogen): 10 mg/mL stock solution in Milli-Q ultrapure water. Gentle sonication speeds the solubilization. Prepare fresh working solution (1 ␮g/mL) in PBS. 6. Paraformaldehyde (PAF): 8% (w/v) stock solution in MilliQ ultrapure water. To help solubilization heat below 60◦ C on a stirring hot plate inside a fume hood, as PFA is toxic. Once dissolved, cool to room temperature for use. Prepare working solution (4% PFA) by mixing equal volumes of 8% PFA and of PBS (2X). 7. Mounting medium: add 10 g of Mowiol 4–88 (Calbiochem, La Jolla, CA, USA) to 90 mL of PBS (pH 7.4) and stir for several hours. Then, add 2.5% DABCO

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(1,4-diazabicyclo[2.2.2]octane) (Sigma) plus 40 mL glycerol and stir overnight. Centrifuge the solution (40,000×g for 30 min), then dispense the clear supernatant into 1–2 mL aliquots and freeze them at –20◦ C until use. Thaw the aliquot at 37◦ C before use. Aliquots may be frozen again. 2.8. Transmission Electron Microscopy

1. HBSS, as described in Step 3 of Section 2.1. 2. PBS (2X), as described in Step 3 of Section 2.7. 3. Glutaraldehyde commercial aqueous solution 25% (v/v): prepare 3% (v/v) solution in PBS fresh for each experiment. Mix equal volumes of the 25% commercial solution and of PBS (2X). Dilute the resulting 12.5% glutaraldehyde solution with PBS (1X) to get a final concentration of 3%. 4. Osmium tetroxide (OsO4 ) (Sigma): Due to its toxicity OsO4 must be manipulated in a fume hood. Prepare an initial 5% (w/v) solution in Milli-Q ultrapure water. Prepare working solution (2.5% w/v) by mixing equal volumes of 5% OsO4 and of PBS (2X). Prepare the solution the day before use, as OsO4 crystals are difficult to dissolve. Store at 4◦ C protected from light. 5. Ethanol solutions: prepare 30, 50, 70, and 90% (v/v) solutions in Milli-Q ultrapure water from ethanol absolute. 6. Propylene oxide (Fluka). 7. 2,4,6-Tri(dimethylamino methyl) phenol (DMP30) (Tousimis, Rockville, MD, USA). 8. Resin A: 6.88 mL of Epon-812 epoxy resin (Tousimis) plus 11.11 mL of dodecenyl succinic anhydride (DDSA) (Tousimis). Prepare in thoroughly cleaned and dried Erlenmeyer flasks. Keep under gentle magnetic stirring until the mixture becomes completely transparent (ca. 30 min). 9. Resin B: 22 mL of Epon-812 plus 19.8 mL methyl-5norbornene-2,3-dicarboxylic anhydride ultrapure (NMA) (Tousimis). Prepare in thoroughly cleaned and dried Erlenmeyer flasks. Keep under gentle magnetic stirring until the mixture becomes completely transparent (ca. 30 min). 10. Mix resins A and B into a single Erlenmeyer flask and keep under gentle magnetic stirring to get a clear, fully transparent mixture (see Note 6). The volumes indicated above have been calculated for a set of 24 samples, prepared in 1.5 mL microcentrifuge tubes. If necessary, adjust volumes to your specific requirements. Manipulation must be carried out in a fume hood. Resins are light sensitive. R 11. Polyethylene BEEM pyramidal capsules (Beem Inc., West Chester, PA, USA).


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12. Lead citrate (Sigma): prepare a 25 mM solution in Milli-Q ultrapure water. Care should be taken due to lead toxicity. 13. Formvar-carbon coated copper grids (Electron Microscopy Sciences, Hatfield, PA, USA). 2.9. Assessment of Leishmania Apoptosis by Flow Cytometry

1. Sterile HBSS, as described in Step 3 of Section 2.1. 2. Sterile RPMI 1640 + HIFCS medium, as described in Step 1 of Section 2.1. 3. PBS (1X), obtained from 2X stock solution (see Step 3 of Section 2.7). 4. Sterile 24-well microplates. 5. N-hexadecylphosphocholine (Anatrace Inc, Maumee, OH, USA): 2 mM stock solution in PBS. Store at –20◦ C. Prepare fresh working solution (30 ␮M) in PBS for each assay (see Note 8). This is used as apoptotic stimulus. 6. Staining solution: 3 mg/mL ribonuclease A (Sigma) plus 50 ␮g/mL propidium iodide (Invitrogen) in PBS (1X). Prepare fresh for each experiment. Consider a 500 ␮L volume for each sample. Shield from direct light exposure. 7. Ethanol solution: 70% (v/v) in Milli-Q ultrapure water from ethanol absolute. Store at 4◦ C.

3. Methods The protocols described below use cell cultures of Leishmania, therefore, it is mandatory a strict follow-up of the safety procedures implemented for pathogen and cell culture handling under sterile conditions in your institution. This includes wearing protective clothes, goggles, and gloves; protocols for the correct disposal of biological residues; adequate training of the personnel; and a laboratory with at least a biosafety level 2. For L. donovani and L. braziliensis, culture and handling regulations may require a level 3 laboratory. 3.1. Cell Culture and Harvesting 3.1.1. Leishmania Culture

1. Cultured Leishmania cells are routinely maintained in 25 cm2 tissue culture flasks. When higher amounts are required, the culture may be scaled up to grow into 1 L Pyrex screw cap bottles on a roller apparatus. 2. Parasite cultures are maintained at 7–15 × 106 parasites/mL in the respective growth medium for each stage, i.e., promastigotes in RPMI 1640 + HIFCS, (see Step 1 of Section 2.1) at 27◦ C (see Note 9), and axenic L. pifanoi amastigotes

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in M199 + HIFCS (see Step 2 of Section 2.1) at 32◦ C (see Note 10). 3.1.2. Leishmania Harvesting

1. Collect parasites at late exponential growth phase (12–15 × 106 cells/mL) by centrifugation at 1,000×g in a clinical centrifuge, decant supernatant carefully, and wash them twice in HBSS at 4◦ C. Resuspend the cells in HBSS at a final density of 4 × 107 cells/mL, and keep on ice. Unless otherwise stated, these conditions must be maintained for the rest of the experiments.

3.1.3. Macrophages

1. The murine macrophage line RAW 264.7 is routinely cultured as a monolayer in the growth medium described in Step 1 of Section 2.1, at 37◦ C, until cellular confluence is reached. 2. For harvesting and subculturing, the culture medium is removed by careful aspiration, avoiding disturbance of the cell monolayer, replaced by cold HBSS, and the culture flask chilled over ice for 15 min. 3. Detachment of macrophages from plastic culture flasks is carried out with a sterile cell scraper. Alternatively, removal of adherent cells can be obtained by washing the cell monolayer with warm (37◦ C) HBSS, and further addition of 1 mL (for a 25 cm2 tissue culture flask) of a sterile solution of 0.25% (w/v) trypsin + 0.2% (w/v) EDTA in RPMI 1640 (without serum). After incubation for 2 min, a massive detachment should be observed in an inverted microscope. Add 10 mL of RPMI + HIFCS (see Step 1 of Section 2.1) to stop further trypsin activity. 4. Transfer the detached macrophages into a 50 mL sterile tube, fill the rest of the tube with sterile RPMI + HIFCS, and centrifuge at 500×g at 4◦ C. Finally, gently resuspend the pellet in the desired volume of complete growth medium and reseed in new tissue culture flasks.

3.2. Cell Proliferation Measurements Following Exposure to AMPs

Cell counting becomes a tedious practice in those studies with a considerable number of samples. In these cases, the colorimetric measurement of viable cells using the chromophore MTT allows an automated quantification of viable cells, at lower cost than other reagents such as Alamar blue (24) or soluble formazan (XTT) (sodium-2,3-bis-[2-methoxy-4-nitro-5-sulfophenyl]-2Htetrazolium-5-carboxanilide) (25), even when both of them allow direct reading of the soluble final product. The method described exploits the ability of mitochondrial dehydrogenases to reduce the yellow-colored MTT to blue, insoluble formazan (26). The amount of formazan is, hence, directly related to the number of viable cells.


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Two complementary method variants following the same procedure may be used, addressing both cell viability (short term) and cell proliferation (long term), which may even use the same sample for the sake of comparison. Whereas in the short-term modality, cell number remains essentially constant and reduction of MTT depends only on viable parasites, in the longterm assay, differential parasite proliferation determines MTT reduction. The protocol is identical for both parasite stages, except for the incubation temperature and growth medium used. 3.2.1. Common Steps

1. Prepare peptide solutions in HBSS at 2X the concentration to be assayed. Sterile conditions must be maintained throughout the whole protocol. 2. In a sterile 96-well microplate, place 60 ␮L/well of the parasite suspension (4 × 107 cells/mL) in HBSS. Then add 60 ␮L/well of the corresponding 2X peptide solutions and mix by pipetting. In order to ensure statistical significance, each point must be assayed in triplicate. Include positive control (nontreated parasites) as well as blank wells without parasites to correct for color background. 3. Incubate the samples for 4 h at 27◦ C or 32◦ C, for promastigotes and amastigotes, respectively.

3.2.2. Protocol for Promastigote Proliferation (Long-Term AMPs Effect)

1. With a multichannel pipette, transfer 20 ␮L aliquot from each well of the plate setup in Step 3 of Section 3.2.1 into another sterile 96-well microplate replica, containing 130 ␮L/well of RPMI 1640 medium devoid of phenol red, supplemented with 10% HIFCS (see Step 2 of Section 2.2). Make sure to mix thoroughly each well before transferring the content in order to obtain a homogeneous cellular suspension. Incubate this microplate for 3 days at 27◦ C, to allow parasite proliferation. 2. Add 50 ␮L of 2 mg/mL MTT solution to each well and incubate at 27◦ C. Wait until a well-developed color appears (ca. 90 min) in the positive control wells (untreated parasites). 3. Add 100 ␮L of 10% (w/v) SDS solution to each well, including those containing the blank, to stop the reaction and dissolve the blue formazan crystals. Full solubilization may take few hours. Incubation of the microplate at 37◦ C speeds up the process. 4. Read absorbance at 600 nm in a microplate reader fitted with a 595 nm filter. A good linear correlation with cell number under this setting was obtained with a 595 nm absorbance between 0.05–0.90.

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3.2.3. Protocol for L. pifanoi Amastigote Proliferation (Long-Term AMPs Effect)

1. Mix thoroughly each well of the plate set up in Step 3 of Section 3.2.1 by pipetting with a multichannel pipette and transfer 20 ␮L from each well into another sterile 96well microplate, containing 130 ␮L/well of M199 + HIFCS medium (see Step 2 of Section 2.1). Incubate this microplate for 5 days at 32◦ C. 2. Transfer the cells from each well into 1.5 mL microcentrifuge tubes. To minimize cell losses, additionally rinse each well with 100 ␮L HBSS and transfer to the respective tubes (see Note 11). 3. Centrifuge the tubes in a microcentrifuge (5 min, maximum speed) and remove supernatant. 4. Add 1 mL of HBSS at 4◦ C to each tube, resuspend the pellet, and centrifuge again as in Step 3 of Section 3.2.3. 5. Remove supernatant and resuspend the cells in 100 ␮L of 0.5 mg/mL MTT solution. 6. Transfer the whole content from each tube to a 96-well microplate. Wait until a well-developed color appears (ca. 2 h) in the positive control wells (untreated amastigotes). 7. Proceed as described in Steps 3 and 4, Section 3.2.2.

3.2.4. Protocol for Promastigote/Amastigote Viability (Short-Term AMPs Effect)

1. Add 100 ␮L per well of 1 mg/mL MTT solution to the plate setup in Step 3 of Section 3.2.1. 2. Incubate at 27◦ C or 32◦ C (for promastigotes and amastigotes, respectively), shielded from light until color appearance. 3. Proceed as described in Steps 3 and 4, Section 3.2.2.

3.3. AMP Cytotoxicity against Intracellular Amastigotes

In the vertebrate host, the amastigote form of Leishmania is an obligate intracellular parasite. This precludes a direct interaction with an exogenous antimicrobial peptide. Hence, in order to ensure the feasibility of a given peptide for its development as a new lead, a further assay of its activity on Leishmania infected macrophages represents a closer approximation to the physiological condition. Direct examination by microscope of the stained slides and intracellular amastigote counting, constitute the easiest way to assess the efficacy of the peptide on parasite burden reduction. A minimum counting of 200 macrophages from different fields, with their respective intracellular parasites, is recommended to ensure statistical significance. The protocol described below must be carried out in a vertical laminar flow hood with sterile material. 1. Collect the macrophages, centrifuge at 500×g and gently resuspend the cellular pellet in fresh RPMI 1640 + HIFCS (see Step 1 of Section 2.1) at 106 cells/mL.


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2. Seed 100 ␮L/well (105 macrophages/well) in a Lab-Tek 16-well chamber slide system. Incubate at 37◦ C for 2 h to allow attachment of the cells to the glass bottom of the slide. 3. Collect amastigotes from their growth flask by centrifugation at 1,000×g and resuspend the pellet in fresh RPMI 1640 + HIFCS medium at a final density of 4 × 106 cells/mL. 4. Remove carefully the medium from the macrophage seeded wells by aspiration, and add immediately 100 ␮L/well of the 4 × 106 cells/mL amastigote suspension through the wall of the well. Avoid dryness of the well (see Note 12). 5. Incubate the multiwell slide at 32◦ C for 4 h to allow phagocytosis of the parasites by macrophages. For amastigotes from species of the donovani complex, incubation and the rest of this procedure must be carried out at 37◦ C (see Note 10). 6. Carefully remove the non-phagocytosed amastigotes by aspiration of the medium from the wells, avoiding perturbation of the macrophage monolayer. Add 100 ␮L per well of warm RPMI 1640 + HIFCS medium and remove again by aspiration. Repeat the same procedure again. Finally, add 300 ␮L per well of the RPMI 1640 medium supplemented with 2% HIFCS and leave at 32◦ C for 4 days to let infection progress. 7. Prepare the peptide solutions at the desired concentration in HBSS (see Note 3). 8. Carefully remove the medium from the wells by aspiration. Add 300 ␮L of warm (32◦ C) HBSS (see Step 3 of Section 2.1), aspirate, and repeat again. 9. After removal of HBSS, add 100 ␮L per well of the corresponding peptide solution and incubate for the time set up by the operator at 32◦ C. 10. After incubation, remove the peptide solution from the wells by aspiration and add 300 ␮L per well of RPMI medium supplemented with 2% HIFCS (see Note 13). 11. Incubate the 16-well chamber slide for 48 h at 32◦ C. 12. Wash the wells twice with 100 ␮L/well of warm (32◦ C) HBSS. 13. Air-dry the slides. 14. Add 100 ␮L of methanol per well, remove it after 1 min, and air-dry the slide. 15. Prepare the Giemsa staining solution by diluting 1 volume of Giemsa stock solution with 20 volumes of distilled water.

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16. Add 100 ␮L of Giemsa staining solution to each well and incubate for 30 min, shielded from light. 17. Rinse the slide with distilled water to remove unspecific cytoplasmic staining of the macrophage. Do not add the water directly to the cell-seeded area as it may detach cells from the preparation. 18. Remove the plastic wells from the slide according to the manufacturer instructions. Make sure to remove any traces of silicone stuck to the slide before adding the mounting medium. Carefully, use a razor blade if necessary. R mounting medium per well 19. Add a single drop of Eukitt and gently place the coverslip over the slide avoiding entrapment of air bubbles. Let dry and observe in an optical light microscope using a 100X oil immersion objective. Slides can be stored at room temperature for months. Calculate the intracellular amastigotes:macrophage ratio. Parasites appear as small violet dots, whereas the macrophage nuclei appear as large, well-stained, irregular, circularshaped structures (see Note 14).

3.4. Assessment of Plasma Membrane Permeabilization by AMPs

Perhaps the most documented attribute of AMPs is their interaction with the plasma membrane phospholipids of the target cell, a common step in their mechanism of action, regardless of their wide variety of primary and secondary structures. For many AMPs, this initial interaction is ensued by insertion into the plasma membrane, disrupting its integrity as a permeability barrier and leading to a fast and lethal disruption of internal homeostasis. However, this scenario is increasingly challenged by evidence of other AMPs whose lethal action involves the recognition of intracellular targets. To exert their action, these peptides will translocate across the plasma membrane, through a transient, frequently nonlethal distortion of its structure (27, 28). In this section, it is described how Leishmania plasma membrane integrity can be assessed by two complementary fluorescence techniques: entrance of vital dyes and assessment of membrane depolarization. The entrance of vital dyes is based on the increase of the fluorescence of cationic dyes, such as propidium iodide and SYTOX Green, once they are bound to intracellular nucleic acids. Entrance of these molecules requires severe damage to the plasma membrane due to their relatively high molecular weight (29–31). However, small, transient membrane lesions, which are not big enough to allow the movement of vital dyes such as SYTOX Green (MW = 600) across the membrane, can be monitored using potential-sensitive fluorescent probes such as bisoxonol. These discrete lesions allow permeation of ions, leading to dissipation of ionic gradients across the plasma membrane and hence plasma membrane depolarization (32).


3.4.1. Entrance of the Vital Dye SYTOX Green

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In this section plasma membrane integrity is assessed by the entrance of the cationic fluorescent vital dye SYTOX Green, which upon nucleic acid binding enhances its fluorescence more than 500-fold (33, 34). 1. Prepare peptide solutions at 10X the desired final concentration in HBSS (see Note 3). 2. Mix equal volumes of the parasite suspension (4 × 107 cells/mL) and of 2 ␮M SYTOX Green solution, as described in Step 1 of Section 2.4.1; incubate for 5 min at 27◦ C for promastigotes or 32◦ C for L. pifanoi amastigotes. 3. Transfer 100 ␮L aliquot per well of the cell suspension obtained in Step 2 into a black polystyrene 96-well microplate. 4. Read fluorescence in a microplate reader, equipped with excitation and emission filters of 485 and 520 nm, respectively. Wait until signal stabilization. Adjust temperature according to the temperature optimal for the specific Leishmania stage being assayed (see Note 10). 5. After fluorescence stabilization, quickly add 10 ␮L per well of the 10X peptide solutions using a multichannel pipette, and record the increase in fluorescence. 6. Finally, add to each well 10 ␮L of 1% (w/v) Triton X-100 solution. Wait till fluorescence readout stabilizes and take this value as the maximal permeabilization for each well.

3.4.2. Plasma Membrane Depolarization

This protocol has been designed to monitor plasma membrane depolarization using the potential-sensitive fluorescent probe bisoxonol. Insertion of this anionic fluorescent molecule in the plasma membrane is precluded by the negative membrane potential. Once the plasma membrane potential decreases, the probe inserts into the lipid bilayer and enhances its fluorescence with a red shift. Increased depolarization results in additional dye insertion and enhanced fluorescence and vice versa. The dynamic outcome of depolarization contrasts with the high-affinity binding of SYTOX Green to nucleic acids, which is close to irreversibility; this is an important difference to keep in mind for the interpretation of results. 1. Prepare working peptide solutions in HBSS (see Note 3) at 10X the desired final concentration. 2. Mix equal volumes of the parasite suspension (4 × 107 cells/mL) and of 0.2 ␮M bisoxonol solution (see Step 1 of Section 2.4.2). Incubate for 5 min at the growth temperature of the specific Leishmania stage assayed (27◦ C for promastigotes, regardless of the species, 32◦ C for L. pifanoi axenic amastigotes).

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3. Transfer 100 ␮L per well of this parasite suspension into black polystyrene 96-well microplates. 4. Read fluorescence in a microplate reader, equipped with excitation and emission filters of 544 and 584 nm, respectively. Wait until signal stabilization. Set up device at the same temperature as in Step 2 of this protocol. 5. After fluorescence stabilization, quickly add 10 ␮L per well of the 10X peptide solutions with a multichannel pipette, and record fluorescence. Refer data to maximal depolarization, obtained after addition of 10 ␮L of 8 ␮M gramicidin D to each well (see Note 5). 3.5. Mitochondrial Membrane Depolarization

One of the parameters more closely related to mitochondrial functionality is the mitochondrial electrochemical potential ( m ). Its depolarization is related to several critical processes within the cell, such as dysfunction of oxidative phosphorylation or the development of apoptosis, since in Leishmania the extrinsic pathway is absent. Changes in the m are caused by equilibration of H+ /OH– gradient across the inner mitochondrial membrane. At short times, the permeabilization of the plasma membrane caused by some AMPs may not be immediately reflected in m values, but it does with those AMPs with a mitochondrial target (35). The variation of m can be easily monitored by using mitochondrial selective fluorescent probes, such as the following protocol, based on the differential accumulation of rhodamine 123 (36). This probe is a cell-permeant, cationic, fluorescent dye that is readily sequestered by metabolically active mitochondria, without significant cytotoxic effects (37). 1. Prepare peptide solutions at 2X the desired final concentration in HBSS (see Note 3). 2. Mix equal volumes of the parasite suspension (4 × 107 cells/mL) and of 2X peptide solution. Incubate in 1.5 mL microcentrifuge tubes at 27◦ C in case of promastigotes or 32◦ C for L. pifanoi amastigotes, for 4 h in both cases. 3. Prepare in duplicate a control sample of fully depolarized parasites by mixing equal volumes of the parasite suspension and of 10 mM KCN solution. Incubate as in Step 2. 4. Wash the parasites by adding 1 mL of HBSS warmed at the corresponding temperature defined in Step 2 of this protocol, and centrifuge 5 min at maximum speed in a microcentrifuge. Repeat this procedure once more. 5. Resuspend the cells in 0.3 ␮g/mL rhodamine 123 solution, at half the volume stated in Step 2 (ca. 4 × 107 cells/mL). Incubate for 10 min in a water bath at 37◦ C, regardless of the parasite stage being assayed, shielded from light.


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6. Leave two control samples of parasites without staining to adjust flow-cytometer background. 7. Wash the parasites twice with HBSS (see Step 3 of Section 2.1) by centrifugation as in Step 4. 8. Resuspend each pellet in 500 ␮L HBSS and transfer to flowcytometer tubes. 9. Measure cell fluorescence in a flow cytometer with excitation and emission wavelengths set at 488 and 520 nm, respectively. 3.6. Oxygen Consumption

In Leishmania, glycolysis plays a minor role within the energy metabolism, being the oxidative phosphorylation, the main source to fulfill the energetic requirements of the parasite (38). Since the electron transfer throughout the respiratory chain is strictly coupled to mitochondrial ATP-synthesis, inhibition of one process will result in inhibition of the other and vice versa, hence the measurement of the oxygen consumption rate constitutes a parameter tightly related to the oxidative phosphorylation. The polarographic measurement of dissolved oxygen is the election technique to monitor oxygen consumption in this protocol. The measurement is carried out in a Clark oxygen electrode (39). The device is composed by a platinum electrode connected by a salt bridge to a solid silver electrode, shielded by a layer of insulating material. A saturated KCl solution is held in place over the surfaces of the electrodes by a teflon membrane. The oxygen monitor holds a constant voltage difference across the two electrodes so that the platinum electrode is negatively charged with respect to the silver electrode. The basic principle of this method relies on the fact that the rate at which electrons leak from the platinum electrode is proportional to the concentration of oxygen available in the sample to receive them, as described in the reaction below. The result is an electrical current converted to a voltage by the oxygen monitor: 4Ag+ + 4Ci− ↔ 4AgCi + 4e− (at the silver electrode) 4H+ + 4e− + O2 ↔ 2H2 O (at the platinum electrode) In order to calculate the oxygen consumption rate, it is possible to use the values for dissolved oxygen reported by Truesdale and Downing (40). The respiration buffer described in Step 1 of Section 2.6, equilibrated with air, in our hands contains 0.237 ␮mol of molecular oxygen per mL at 25◦ C (pH 7.4). 1. Set up the Clark electrode following the manufacturer instructions. Note that the electrode needs to be polarized several hours prior to its use.

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2. Adjust the temperature of the Clark electrode chamber at 25◦ C by connecting the jacket into a water circulating bath at the desired temperature. 3. Keep the respiration buffer at the desired temperature (e.g., 25◦ C for promastigotes) in constant equilibrium with air. For this purpose, maintain the buffer in an open recipient partially immersed in a water bath at the set-up temperature. 4. Collect parasites at late exponential phase by centrifugation as described in Section 3.1.2, and wash them twice by centrifugation at 1,000×g in respiration buffer at 4◦ C. 5. Resuspend the pellet at a final density of 109 cells/mL in respiration buffer and keep this cellular suspension in ice. 6. Pipette 0.9 mL of respiration buffer into the Clark electrode chamber. 7. Add 100 ␮L of the parasite suspension prepared in Step 5. Close the chamber immediately to avoid replenishment of consumed oxygen by air. 8. Record the oxygen consumption rate before and after the addition of the peptides under study. 3.7. Confocal Microscopy

The confocal microscopy is the technique of choice to localize the subcellular destination for a given fluorescent-tagged peptide. For AMPs this is especially important to unveil the existence of putative intracellular targets. The key feature of confocal microscopy is its capability to produce in-focus images of relatively thick specimens by selectively collecting light from thin (∼1 ␮m) optical sections, rejecting fluorescent light from other planes within the specimen (41, 42). It is especially useful for co-localization studies by the simultaneous use of several dyes, provided that their respective fluorescence spectra do not overlap. In these experiments, organelle(s) is(are) selectively stained with a specific fluorescent probe and compared with the distribution pattern of a peptide coupled to a different fluorescence tag (35). The protocol presented herein was designed for a colocalization assay, using three different fluorophores: a fluoresceinated AMP (λex 488 nm, λem 520 nm), MitoTracker Red (λex 578 nm, λem 599 nm) for specific mitochondrial staining, and DAPI (λex 358 nm, λem 461 nm) as a nuclear and kinetoplast dye. 1. Mix equal volumes of the 4 × 107 cells/mL parasite suspension with 0.1 ␮M MitoTracker Red solution as described in Step 4 of Section 2.7 (see Note 15). Incubate in darkness for 10 min at 27◦ C or 32◦ C in case of promastigotes or amastigotes, respectively. 2. Eliminate the unbound dye from the medium by parasite centrifugation (10 min at 1,000×g) and further removal


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of the supernatant by aspiration. Wash the resulting pellet as above by adding the same volume of HBSS (described in Step 3 of Section 2.1). Resuspend the cell pellet to a density of 4 × 107 cells/mL in HBSS. 3. Prepare fluorescein-labelled peptide solutions in HBSS at 2X the desired final concentration (see Note 3). 4. Mix equal volumes of the parasite suspension (4 × 107 cells/mL) and of 2X fluorescein-labelled peptide solution in microcentrifuge tubes. Incubate at 27◦ C for promastigotes, or at 32◦ C for amastigotes, for a period of time required by the designed experiment. 5. Stop peptide–cell interaction by adding 1 mL PBS (1X) at 4◦ C. Centrifuge immediately the parasites for 5 min at maximum speed in a microcentrifuge and remove the supernatant by aspiration. Repeat the whole procedure described in this step once more, but leave 10–15 ␮L of the last supernatant in the microcentrifuge tube. 6. Resuspend the pellet in the remaining 10–15 ␮L of PBS, in order to obtain a homogeneous cell suspension, as after fixation cellular aggregation becomes irreversible. It is therefore essential to have a monodisperse cell suspension prior to fixing the cells with paraformaldehyde during the next step. 7. Add to each tube 100 ␮L of 4% PFA solution in PBS to fix the cells, and keep at room temperature for 20 min. 8. Stop fixation and remove PFA by addition of 1 mL PBS (1X). Spin down parasites by centrifugation for 5 min at maximum speed in a microcentrifuge and remove supernatant. Repeat this step once more. 9. Add to each tube 100 ␮L of 1 ␮g/mL DAPI solution in PBS. Incubate at room temperature for 40 min. 10. Wash twice by adding 1 mL of PBS (1X). Collect the parasites as in Step 8 of this protocol. Resuspend the pellet in 30 ␮L PBS. 11. On a printed microscope slide, pipette 10 ␮L of each sample per well and air-dry. 12. Add one drop of Mowiol per well, and gently place the coverslip over the slide, avoiding trapping air bubbles. Let it dry and observe under a confocal laser scanning microscope at the corresponding wavelengths, using a 63X oil immersion objective. Dried slides can be stored at 4◦ C for 30 days. 3.8. Transmission Electron Microscopy

Transmission electron microscopy (TEM) constitutes an excellent tool to observe ultrastructural alterations in Leishmania at a thousand times higher magnification than that provided by optical

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microscopy. Two implicit technical requirements are the obtainment of ultrathin sections, as the specimen must be of such a low density to allow electrons to pass through the tissue, and the use of a heavy metal to contrast the subcellular structures. The protocol described below requires 5 days to obtain the final epoxy resin blocks ready for processing in the ultramicrotome. Since the TEM works in vacuum, the water contained in the sample must be removed by a gradual dehydration with ethanol. The previous fixation of the cells prevents the disruption of subcellular structures due to dehydration. Sample embedding in the resin must be done gradually, by a progressive increase of the resin percentage into the sample. 1. Prepare peptide solutions in HBSS at 2X the desired final concentration (see Note 3). Estimate an approximate volume of 500 ␮L per sample tube. 2. Mix equal volumes (500 ␮L each) of the parasite suspension (4 × 107 cells/mL) and of the 2X peptide solution. A final volume of 1 mL per sample tube is recommended to ensure an optimal parasite number, as loss of cellular material is frequent through the long procedure. Incubate at 27◦ C or 32◦ C for promastigotes or L. pifanoi axenic amastigotes, respectively, in microcentrifuge tubes for the desired time (see Note 16). 3. Spin down the parasites by centrifugation in a microcentrifuge (5 min at full speed). 4. Remove the supernatant by aspiration and resuspend the pellet into 1 mL of PBS (1X). Centrifuge the samples for 5 min at maximum speed in a microcentrifuge. Repeat this step once more (see Note 17). 5. Resuspend the cellular pellet in the remaining 15 ␮L of PBS in order to obtain a monodisperse cellular suspension. Parasite clumping will be irreversible after fixation, precluding observation of individual cells at the end of the process. 6. Add to each tube 100 ␮L of a 3% glutaraldehyde solution in PBS (described in Step 3 of Section 2.8) to fix the cells. Incubate samples at room temperature for 90 min. 7. Spin down the cells and wash them as in Step 4 of this protocol; resuspend the pellet in the remaining 15 ␮L avoiding formation of aggregates. 8. Add to each tube 100 ␮L of a 2.5% OsO4 solution in PBS (described in Step 4 of Section 2.8); incubate at room temperature for 90 min. 9. Spin down the cells and wash them as in Step 4 of this protocol; resuspend the pellet in the remaining 15 ␮L avoiding formation of aggregates.


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10. Add to each tube 1.5 mL of 30% ethanol. Incubate for 30 min at room temperature. 11. Pellet the cells by 5 min centrifugation at maximum speed in a microcentrifuge. Remove carefully the supernatant by aspiration. 12. Add to each tube 1.5 mL of 50% ethanol. Do not resuspend the pellet. Incubate at room temperature for 30 min and proceed as in Step 11 to pellet the cells. 13. Add to each tube 1.5 mL of 70% ethanol. Do not resuspend the pellet. Incubate for 30 min at room temperature. Once in 70% ethanol, samples can be stored overnight at room temperature. 14. Proceed as in Step 11 to collect parasites. Add to each tube 1.5 mL of 90% ethanol. Do not resuspend the pellet. Incubate at room temperature for 30 min and repeat Step 11. 15. Add to each tube 1.5 mL of absolute ethanol. Do not resuspend the pellet. Keep at room temperature for 30 min and proceed as in Step 11. 16. Add to each tube 0.5 mL of propylene oxide. Do not resuspend the pellet. Keep at room temperature for 1 h. Repeat Step 11. At this point, all traces of water have been removed from the sample, so care should be taken to avoid contact with wet material. This, and all the following steps involving propylene oxide handling, must be carried out inside a fume hood due to the toxicity and volatility of this reagent. 17. Add to each tube 0.5 mL of a solution 3:1 (v/v) propylene oxide:resin (A+B). Do not resuspend the pellet. Incubate at room temperature for 30 min. Prepare the solution 5 min before use. To avoid propylene oxide evaporation, add this reagent over resin (A+B), and keep the solution in a covered flask under soft magnetic stirring until its immediate use. Proceed as in Step 11. 18. Add to each tube 0.5 mL of a freshly prepared solution 1:1 (v/v) propylene oxide:resin (A+B). Do not resuspend pellet. Incubate at room temperature for 30 min. Repeat Step 11. 19. Add to each tube 0.5 mL of a freshly prepared solution 1:3 (v/v) propylene oxide:resin (A+B). Do not resuspend the pellet. Incubate at room temperature for 30 min. Repeat Step 11. If necessary, at this step samples can be stored at room temperature overnight. 20. Pour into each tube 0.5 mL of resin (A+B). Do not resuspend the pellet. Incubate at room temperature for 30 min. Repeat Step 11. Leave 100 ␮L of the supernatant at the bottom of each tube.

412


21. Prepare freshly a solution by mixing 0.18 mL DMP30 with 10 mL resin (A+B). Keep under soft magnetic stirring. 22. Carefully transfer the cell pellet from the microcentrifuge R pyramidal capsules. As tubes into polyethylene BEEM this reagent is quite viscous, facilitate transfer by using tips truncated at their end, by cutting with a razor blade. Try to position the pellet as close as possible to the bottom of the capsules. 23. Fill the capsules with the DMP30-resin (A+B) mixture prepared in Step 21, avoiding bubble formation. 24. Close each capsule with its cap and place them carefully with the apex facing down, into 1.5 mL microcentrifuge tubes. Centrifuge at 1,000 × g for 20 min in order to pellet the cells at the apex of the pyramidal capsule. To prevent damage of the capsules during centrifugation, a small piece of cotton should be placed at the bottom of the microcentrifuge tubes, so capsules lay over the cotton. 25. Open the capsules, transfer into an appropriate holder and keep them at 70◦ C for 48 h to allow resin polymerization. 26. Use an ultramicrotome with a gem quality diamond knife to obtain ultrathin sections (6 h), it is recommended to carry out this step in sterile conditions; if longer, substitute the defined medium for full growth medium, RPMI 1640 + HIFCS for promastigotes (see Step 1 of Section 2.1), or M199 + HIFCS medium for L. pifanoi amastigotes (see Step 2 of Section 2.1). Be aware of the strong inhibition of the peptide by serum components. It is important to realize that comparison between inhibition of viability/proliferation and subsequent morphological damages and other effects will require identical conditions (time, incubation medium, etc.) in order to draw valid conclusions. An alternative is the use of serumfree culture medium as described for other eukaryotic cells. 17. Due to the high number of steps involving centrifugation and supernatant removal, do not remove the supernatant

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exhaustively in order to preserve the pellet. Leave at least 15 ␮L of supernatant to preclude cell losses throughout the process.

Acknowledgments This work was supported by research grants from the Consejo Superior de Investigaciones Cient´ıficas (CSIC; PIF 80F0171), ´ Sanitaria (FIS PI06115, PS09/01928 Fondo de Investigacion and RD 06/0021/0006), Ministry of Science and Innovation PET 2006–0139-01, and European Union (HEALTH-F3–2008223414). The careful editing of the manuscript by Prof. David Andreu, Pompeu Fabra University, is gratefully acknowledged. References 1. Udomsangpetch, R., Kaneko, O., Chotivanich, K., and Sattabongkot, J. (2008) Cultivation of Plasmodium vivax. Trends Parasitol. 24, 85–88. 2. Hotez, P. J., Molyneux, D. H., Fenwick, A., Kumaresan, J., Sachs, S. E., Sachs, J. D., and Savioli, L. (2007) Control of neglected tropical diseases. N. Engl. J. Med. 357, 1018– 1027. 3. Kima, P. E. (2007) The amastigote forms of Leishmania are experts at exploiting host cell processes to establish infection and persist. Int. J. Parasitol. 37, 1087–1096. 4. Pays, E., Vanhollebeke, B., Vanhamme, L., Paturiaux-Hanocq, F., Nolan, D. P., and Perez-Morga, D. (2006) The trypanolytic factor of human serum. Nat. Rev. Microbiol. 4, 477–486. 5. Lang, C., Gross, U., and Luder, C. G. (2007) Subversion of innate and adaptive immune responses by Toxoplasma gondii. Parasitol. Res. 100, 191–203. 6. Bogdan, C. (2008) Mechanisms and consequences of persistence of intracellular pathogens: leishmaniasis as an example. Cell Microbiol. 10, 1221–1234. 7. McConville, M. J. and Ralton, J. E. (1997) Developmentally regulated changes in the cell surface architecture of Leishmania parasites. Behring Inst. Mitt. 99, 34–43. 8. Banuls, A. L., Hide, M., and Prugnolle, F. (2007) Leishmania and the leishmaniases: a parasite genetic update and advances in taxonomy, epidemiology and pathogenicity in humans. Adv. Parasitol. 64, 1–109.

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SUBJECT INDEX

A

Bordetella bronchiseptica . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 373 Broth microdilution methodology. . . . . . . . . . . . . . . . . . . . .40

Acetylation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91, 93 Acid-urea polyacrylamide gel electrophoresis (AU-PAGE) . . . . . . . . . . . . . . . . . . . 50–51, 55–57 Acinetobacter baumannii . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 310 Acne infection model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 366 lesions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 307 rosacea . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 307, 321, 339 vulgaris . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 307, 366 Actinomycetes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37, 42 Actinoplanes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 Activity anti-endotoxin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148, 151 anti-infective . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138, 306 anti-inflammatory/anti-endotoxic . . . . . . . . . . . 148, 151, 334–335, 349–357 anti-parasitic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 332–333 Airway epithelial cells . . . . . . . . . . . . . . . . . 372–375, 377, 380 Airway surface fluid antimicrobial assay . . . . . . . . . . . . . . 375 Alamethicin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184, 193–198 Amastigote, see Leishmania Amyloid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194, 199 Animal models . . . . . . . . . 141, 150, 152, 318–320, 341–342 Anti-inflammatory . . . . . . . . . . 141, 307, 313–314, 334–336, 339–340, 349–357 Antimalarial peptidomimetic . . . . . . . . . . . . . . . . . . . . . . . . 317 Antimicrobial peptides (AMPs) development . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80, 85, 402 interactions . . . . . . . 80–81, 89, 138–139, 142, 145, 147, 149, 171–180 isolation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31–43 Apoptosis . . . . . 312–313, 318, 334, 395, 399, 406, 412–414 Arenicin-1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144, 146–147 Artificial neural network (ANN) . . . . . . . . . . . . . . . . . . 82–85 Atomic force microscopy (AFM). . . . . . . 193, 196, 235–246 Atopic dermatitis (AD) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 307

C Calcein . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158, 163, 172–180 Candida albicans . . . . . . . . . . . . . . . . . . . . . . . . . . . 20, 306, 360 Carboxyfluorescein (CF) . . . . . . . . . 158–160, 162–166, 172, 228, 310 Cathelicidins . . . 47, 148, 150, 305, 310–311, 313–314, 374 Cation exchange-HPLC . . . . . . . . . . . . . . . . . . . 16–17, 28–29 Cationic peptides . . . . . . . . . 55, 71, 142–143, 149–150, 212, 235–236, 305, 333, 369 Cationic steroid antibiotics (CSAs) . . . . . . . . . 315, 318, 341 CD14 . . . . . . . . . . . . . . . . . . . . . . . . . . 138, 142–143, 147–148 Cellulose membranes . . . 112–116, 119–120, 128–129, 132 Cholesterol . . . . . . . . . . . . . . . . . 173, 177, 179–180, 196, 228 Circular dichroism (CD) . . . . . . . 4, 156, 187, 190, 303, 351 Clark oxygen electrode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .407 Clinical trials . . . . . . . 33, 141, 150, 316–317, 321–322, 336, 339–340, 366 Cloning . . . . . . . . . . . . . . . . . . . . . . . . . . . 48–49, 52–53, 58, 69 CNBr cleavage . . . . . . . . . . . . . . . . . . . . . . . . . . . 52, 54–56, 65 Competence stimulating peptide (CSP) . . . . . . . . . 383–385, 387–390 Confocal scanning laser microscopy (CSLM) . . . . . . . . 384, 386–387, 390 Contact mode, see Atomic force microscopy (AFM) Critical point drying (CPD) . . . . . . . . . . . 253, 257–258, 264 Cross-resistance . . . . . . . . . . . . . . . . . . . . . . . 40, 317, 319–321 5-cyano-2, 3-ditolyl tetrazolium chloride (CTC) . . . . . 250, 252, 255–256 Cyanogen bromide (CNBr) . . . . . 50, 52, 54–55, 58, 63–65, 68, 71–74

D D-amino acids . . . . . . 78, 103, 143–144, 194, 309–310, 313 Defensins . . . . . . . . . . . . 28, 47–58, 305, 307, 309–314, 318, 321–322, 332–335, 338, 341, 374 Dermatitis model allergic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 350–353 irritant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 350–352 4, 6-diamidino-2-phenylindole (DAPI) . . . . . . . . . 250, 252, 255–256, 397, 408–409 DiSC3–5 . . . . . . . . . . . . . . . . . . . . . . . 172–173, 175, 178–180 Dodecylphosphocholine (DPC) . . . . . . . . . . . . 275–276, 304 Drotrecogin alfa activated (DrotAA) . . . . . . . . . . . . . . . . . 141 Dye efflux kinetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164–165

B Bacillus subtilis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36, 174 Bacterial cell membrane . . . . . . . . . . . . . . . . . . . . 48, 322, 341 Bacterial culture . . . . . . . . . . . 9, 67, 130, 178, 239–240, 245, 251–254, 368, 387 Bactericidal permeability increasing protein (BPI) . . . . 151, 305, 336, 340 Bicelles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187–188, 190 Biofilm assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 385–389 Bis-(1, 3-diethylthiobarbituric) trimethine oxonol (Bisoxonol) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 396 BODIPY TR cadaverine (BC) . . . . . . . . 145, 310, 314, 317, 336–337, 339–340

E Ear inflammation model . . . . . . . . . . 349–350, 352, 355–356 E.coli expression vector . . . . . . . . . . . . . . . . . . . . . . . . . . . 68–70

A. Giuliani, A.C. Rinaldi (eds.), Antimicrobial Peptides, Methods in Molecular Biology 618, c Springer Science+Business Media, LLC 2010 DOI 10.1007/978-1-60761-594-1,

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ANTIMICROBIAL PEPTIDES

422 Subject Index

Edman degradation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5 Electrospray Ionization Mass Spectrometry (ESI-MS) . . . . . . . 17, 19, 21–23, 25, 27–29, 90, 94–95, 104 Endotoxaemia . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 Endotoxin . . . . . . . . . . . . . . . . . . . . . . 138–143, 147–152, 314 Enterobacter cloacae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37, 360 Epithelial cells . . . . . . . . . . . . . . 309, 311, 372, 374, 377, 380 Escherichia coli (E.coli) . . . . . . . . . 4–5, 20, 35, 47–58, 62, 88, 140, 145, 174, 239, 250, 306, 360 Ex vivo skin infection model . . . . . . . . . . . . . . . . . . . . 359–369

F FITC-labeled dextrans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172 Flow cytometry . . . . . . . . . . . . . . . . . . . . . . 147, 399, 412–414 Fluorescein isothiocyanate (FITC) . . . . 148, 172, 250, 252, 255–256 Fluorescence microscopy . . . . . . . . . . . . . . 250–251, 254–256 Fluorescent dyes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172 Förster resonance energy transfer (FRET) . . . . . . . 146–147, 156–158, 164, 166 Frog skin secretions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3–13 Fungi . . . 3–4, 111–112, 304, 308–311, 314, 317–318, 320, 353–354, 360, 362, 364 Fusion proteins . . . . . . . . . . . . . . . . . . . . . . . . 50, 52–55, 62, 70

G Gingival epithelial cell culture . . . . . . . . . . . . . . 373, 377–379 Gramicidin . . . . . . . . 186–188, 193–197, 202, 397, 406, 415 Gram-negative . . . . 4, 41, 87–108, 111, 126, 139–142, 145, 149–151, 174, 178, 199, 235–236, 239, 244, 287, 306, 310–311, 315, 322, 341, 353–354, 360, 390, 394 Gram-positive . . . . . . 4, 32, 40–41, 111–112, 126, 138, 174, 245, 287, 307–308, 315, 321–322, 330, 336, 338, 341, 353–354, 360, 383–384, 390, 394 Granular glands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

H High sensitivity isothermal titration calorimeter . . . . . . . . 91 High-throughput screening . . . . . . . . . . . . . . . . . . . . . 125–133 Histatins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 305, 309 HLF1–11 . . . . . . . . . . . . . . . . . . . . . . . . . . . 314, 316, 337, 340 Host defence peptides (HDPs) . . . . . . . . . . . . 303–315, 317, 319–320, 322, 329–342 HPLC C2/C18-RP-HPLC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 R Cation Exchange . . . . . . . . . . . . . . . . 21 micro-MonoS RP-8-HPLC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20–21 Human skin . . . . . . . . . . . . . . . . . . 15–29, 306–307, 359–360 Hylarana picturata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

I Immunomodulation . . . . . 142, 151–152, 313–314, 329–342 Immunostimulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142, 151 Infections blood stream . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141 burn-related . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 317 catheter-related blood stream . . . . . . . . . . . . . . . . . . . . 317 cutaneous . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 306–308 diabetic foot ulcer . . . . . . . . . . . . . . . . . . . . . . . . . . 308, 316 genital . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311 hospital-acquired . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 310

respiratory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 330 soft tissue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321 surgical site . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 340 wound . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 308, 319 Inflammation chronic . . . . . . . . . . . . . . . . . . . . . . . . . . 307, 310, 331, 333 LPS-induced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 319 oxazolone-induced . . . . . . . . . . . . . . . . . . . . . . . . . 354–355 Innate immunity . . . . . . . . . 4, 320, 330–331, 333, 337, 340, 342, 394 In silico design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 288 Isothermal titration calorimetry (ITC) . . . . . . 88–89, 91–92, 95–100, 106–108, 156

K Keratinocytes. . . . . . . . . . . . . . . . . . . . . . . . . . .15–16, 306–308 Keratinocyte serum-free medium (KSFM) . . 373, 377–378 Ketosteroid isomerase (KSI) fusion protein . . . . . 62–63, 65, 67, 69–70

L β-lactamases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37–39, 69 Lactobacillus spp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 Lantibiotics biosynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32, 34–35 evaluation of activity . . . . . . . . . . . . . . . . . . . . . . . . . . 39–42 mode of action . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33–34 Leishmania . . . . . . . . . . . . 394–395, 399–400, 402, 404–407, 409–417 Limulus anti-LPS factor (LALF) . . . . . . . . . . . . . . . . . . . . 151 Limulus test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151 Lipid large unilamellar vesicles (LUVs) . . . . . 107, 158, 160, 162–164, 172–177 Lipopolysaccharide (LPS) binding peptides . . . . . . . . . . . . . . . . . . . . . . . 144, 147, 151 binding protein (LBP). . . . . . . .138–139, 142–143, 145, 149, 151 neutralization . . . . . . . . . . . . . . . . . . . . . . . . . 145, 147–150 LL-37 . . . . . . . 144, 147–149, 305–309, 311–314, 317–318, 332–335, 340, 373, 375–376 LPS-binding protein (LBP) . . . . . . 138–139, 142–143, 145, 149–151 Luminescence . . . . . . . . . . 127, 130–133, 288, 290, 293, 298 Lysozyme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25, 28, 305, 311

M Macrophages . . . . . . 138, 147–149, 151, 334, 395–396, 400, 402–403, 415–417 Magainin . . . . . . . . . . . . . . 147–148, 184, 186, 195, 198–199, 202, 209–210, 212–213, 216–217, 273, 308–309, 313, 339, 341 MALDI-TOF mass spectrometry . . . . . . . . . . . . . . . 5, 52, 57 Mass spectrometry . . . . 5, 12, 17, 19, 22–23, 39, 52, 57, 90, 95, 385 Mellitin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 315 Membrane(s) depolarization . . 174–175, 178–179, 396–397, 404–407 non-oriented, see Nuclear magnetic resonance (NMR) oriented, see Nuclear magnetic resonance (NMR) potential . . . . . . . . . . . . 172–173, 179–180, 313, 405, 417 Methicillin-resistant Staphylococcus aureus (MRSA) . . . . . . . 40–41, 126, 318–320, 336, 340 7-methoxycoumarin-3-carboxylic acid (7MC) . . . 156–157, 159–162, 164–167

ANTIMICROBIAL PEPTIDES Subject Index 423 Micelles . . . . . . . . . 88, 95–96, 146, 155–156, 185, 187–188, 198, 244, 274–276, 281–283, 415 Mimetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88, 309, 322 Minimum inhibitory concentration (MIC) . . . . . . . . 13, 36, 40–41, 43, 79–80, 241, 262, 288, 293, 321 Molecular descriptors . . . . . . . . . . . . 287–288, 293–295, 298 Molecular dynamics atomistic simulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275 CHARMM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269 coarse-grained simulations . . . . . . . . . . . . . . . . . . . . . . . 273 implicit solvation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 273 NAMD . . . . . . . . . . . . . . . . . . . . . 269, 271–272, 276–282 Moraxella catarrhalis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 Mueller Hinton Agar (MHA) . . . . . . . . . . . . . . . . . . . . 36, 41 Mueller Hinton Broth (MHB) . . . . . . . . 6, 9–10, 35–36, 41, 174, 178 Multilamellar vesicles (MLVs) . . . . . . . . . 98, 106, 158, 162, 175–176, 216 Mycobacterium smegmatis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35, 41 tuberculosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

N Neisseria gonorrhoeae . . . . . . . . . . . . . . . . . . . . . . . 306, 311–312 Neutrophils . . . . . . . . . 57, 138, 144, 149, 304–308, 310, 334 Norepinephrine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4–7, 10–11 Nsin Nuclear magnetic resonance (NMR) 13 C . . . 63, 188, 191, 210, 212–215, 217–219, 225–230 15 N . . . 63, 188, 191, 209–215, 217–219, 222–227, 230 19 F . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191–195 2 H . . . . . . . . . . . . . . . . . . 63, 188, 192, 194, 210–220, 222 31 P . . . . . . . . . . . . . . . . . . . . . 212, 214–215, 225, 227–231 magic angle spinning (MAS) . . . . . . 188, 210–211, 214, 217, 224–229, 231 measurements . . . . . . . . . . . 190, 196, 211–214, 217–229 non-oriented membranes . . . . . . . . . . . . . . . . . . . 212–214 oriented membranes . . . . . . . . . . 210, 212–213, 217–220 solid-state . . . . . . 63, 187–188, 190–191, 194–197, 199, 209–231 spectra . . . . . . . . . . . . . . . . . . 209–210, 213, 219–225, 230

O Oligo-acyl-lysines (OAKs) . . . . . . . . . . . . . . . . . . . . . . . . . . 317 Oligomers, see Antimalarial peptidomimetic Omiganan . . . . . . . . . . . . . 309, 317–318, 336, 339, 366–367 Oral bacteria . . . . . . . . . . . . . . . . . . . . . . . . . . 384, 386–387, 391 candidiasis . . . . . . . . . . . . . . 309–312, 321, 336, 339–340 Ovine cathelicidin SMAP-29 . . . . . . . . . . . . . . . . . . . . . . . 308 Ovispirin-1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 308 Oxazolone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 349–357

P Palmitoyloleoylphosphatidylcholine (POPC) . . . . . . . 91, 97, 100–101, 104–106, 157, 159–160, 162, 165, 173, 179–180, 197, 214–219, 228 Palmitoyloleoylphosphatidylethanolamine (POPE) . . . . . . . . . 156–157, 159–162, 164–167, 179–180, 275 1-palmitoyl-2-oleoylphosphatidylethanolamine, see Palmitoyloleoylphosphatidylethanolamine (POPE)

Palmitoyloleoylphosphatidylglycerol (POPG) . . . . . . 91, 97, 101, 104–106, 146, 160, 167, 173, 179–180, 275 Paneth cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48, 57, 311 Peptide alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188–189, 191 antimicrobial assays . . . . . . . . . . . . . . . . . . . . . . . . 198–199 array . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118–119 binding to membranes . . . . . 11, 88, 101, 104, 146–147, 187, 194, 197, 200–202 conformation . . . . . . . . . . . . 186–188, 190, 274–275, 281 cyclic . . . . . . . . . . . 88, 90–93, 95, 97, 100–101, 104, 106, 151–152, 187, 189 design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77–85, 297–298 interaction with membranes . . . . . . . . . . . . 197, 293–294 LPS-binding . . . . . . . . . . . . . . . . . . . . . . . . . . 144, 147, 151 LPS neutralization . . . . . . . . . . . . . . . . . . . . . 145, 147–150 orientation . . . . . . . . . . . . . . . . . . . . . . . 189–190, 196–197 purification . . . . . . . . . . . . . . . . . 5, 8–9, 15–29, 55–57, 95 recombinant . . . . . . . . . . . . . . . . . . . . . . . . . . 56–58, 61–74 reconstitution . . . . . . . . . . . . . . . . . . . . . . . . . 187, 212–219 structure . . . . . . . . . . . . . 5, 77–85, 88, 186–189, 283, 306 synthesis . . . . . . . . . . 85, 90, 92, 100, 102, 117, 126, 335, 384–385 Peptidomimetics . . . . . . . . . . . . . . . . 151, 171, 174–175, 180, 317, 338 PET vector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 Pexiganan . . . . . . . . . . . . . . . . . . . . . . . . . . . 308, 315–316, 339 PG-1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 310 PGLa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184, 192–199, 202 Phosphorus assay . . . . . . . . . . . . . . . . . . . . . . . . . 174, 176–177 Pig skin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 360–362, 364–367 Plectasin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321, 336–338 Polymyxins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145, 310 PR-39 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144, 149, 305, 307 Promastigote, see Leishmania Propionibacterium acnes . . . . . . . . . . . . . . . . . . . . . 36, 307, 360 Proteus mirabilis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146 Pseudomonas aeruginosa . . . . . . . . . . . . 26, 126, 239, 310, 373

Q Quantitative structure–activity relationship (QSAR) . . . . . . . . . . . . . . . . 77–85, 274, 287–290 Quorum sensing (QS) . . . . . . . . . . . . . . . . . . . . . . . . . 383–392

R Radial diffusion antimicrobial activity assay . . . . . . . . . 21–22 Rana temporaria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144–145 Rat intra-abdominal sepsis model . . . . . . . . . . . . . . . . . . . . 314 Recombinant expression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63 Retrocyclins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 312 Reversed-phase HPLC (RP-HPLC) . . . . . . . . . . . 4–5, 7–9, 16–17, 21, 24–25, 27–28, 51, 54–57, 68, 71–73, 90, 94–95, 104, 385 Rosacea . . . . . . . . . . . . . . . . . . . . . . . . 307, 318, 321, 335–336, 339–340

S Saccharomyces cerevisiae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 309 Salmonella enterica . . . . . . . . . . . . . . . . . . . . . . . . . 146–147, 340 Scanning electron microscopy (SEM) . . . . . . . . . . . 251–253, 256–259, 376 SDS-PAGE . . . . . . . . . . . . . . . . . . . . . . . . . . 17–19, 22, 28, 67

ANTIMICROBIAL PEPTIDES

424 Subject Index

Sepsis . . . . . . . . 137–141, 143, 149–152, 313–314, 316, 319 Septic shock . . 137–139, 141, 147–150, 152, 235–236, 319 Serratia marcescens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 360 Sexually transmitted infections (STIs) . . . . . . . . . . . 311–312 β-sheets . . . . . . . 78, 144, 146, 193–194, 197, 303, 322, 337 Skin immunity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 306 infection model . . . . . . . . . . . . . . . . . . . 320–321, 359–369 Small unilamelar vesicles (SUVs) . . . . . . . . . 91, 97–99, 104, 106–107 Solid-phase synthesis . . . . . . . . . . . . . . . . . . . . . 48, 92–94, 335 SPOT synthesis . . . . . . . . . . . . . . . . . . . . . . 112–114, 117–120 Staphylococcus aureus . . . . . 4, 20, 35, 126, 306, 336, 340, 360 Stratum corneum . . . . . . . . . . . . . . . . . . . 5, 16, 18, 20, 24–27 Streptococcus mutans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 384, 388–391 pyogenes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35, 306, 320 Support vector machines (SVM) . . . . . . . . . . . . . . . . . . 82–85 Sushi peptides . . . . . . . . . . . . . . . . . . . . . . . 145–146, 151, 236 SYTOX Green . . . . . . . . . . . . . . . . . . . . . . . . . . . 396, 404–405

Temporin. . . . . . . . . . . . . . .10, 144–145, 148–149, 199, 250, 256, 259 12-o-tetradecanoylphorbol acetate (TPA). . . . . . . .349–350, 352–357 Thermodynamic characterization . . . . . . . . . . . . . . . . . 87–108 TNF-α . . . . . . . . . . . . . . . . . . . . . . . . . 138, 147–149, 151, 320 Topical microbicides. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .311 Transmembrane potential . . . . . . . . . . . . . . . . . . . . . . . . . . . 172 Transmission electron microscopy (TEM). . . . . . . . . . . .251, 253–254, 256–262, 265–266, 395, 398–399, 409–412 Triple-staining method . . . . . . . . . . . . . . . . . . . . . . . . . 250–251 Tryptophan fluorescence . . . . . . . . . . . . . . . . . . . . . . . 146–147

T

Wound healing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335

Talactoferrin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 316 Tapping mode, see Atomic force microscopy (AFM)

V Vancomycin-resistant Enterococcus (VRE) . . . 126, 320–321 Vancomycin-resistant S. aureus (VRSA) . . . . . . . . . . 315, 318

W Z Zinzade reagent . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161

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